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Full wwPDB X-ray Structure Validation Report

O
i

Feb 28, 2014 07:20 PM GMT


PDB ID : 1HHO
Title : STRUCTURE OF HUMAN OXYHAEMOGLOBIN AT 2.1 ANGSTROMS
RESOLUTION
Authors : Shaanan, B.
Deposited on : 1983-06-10
Resolution : 2.10
A(reported)
This is a full wwPDB validation report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
A user guide is available at http://wwpdb.org/ValidationPDFNotes.html

The following versions of software and data (see references) were used in the production of this report:
MolProbity
Mogul
Xtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

:
:
:
:
:
:
:
:
:
:

4.02b-467
1.15 2013
dev-1323
stable22639
21963
5.8.0049
6.3.0 (Settle)
Engh & Huber (2001)
Parkinson et. al. (1996)
stable22683

Page 2

Full wwPDB X-ray Structure Validation Report

Overall quality at a glance

1HHO

The reported resolution of this entry is 2.10


A.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in
the following graphic. The table shows the number of entries on which the scores are based.

Metric
Clashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers

Whole archive
(#Entries)
79885
78287
78261
66119

Similar resolution
(#Entries, resolution range(
A))
3649 (2.10-2.10)
3610 (2.10-2.10)
3611 (2.10-2.10)
3013 (2.10-2.10)

The table below summarises the geometric issues observed across the polymeric chains and their fit
to the electron density. The red, orange, yellow and green segments on the lower bar indicate the
fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria.
The upper red bar (where present) indicates the fraction of residues that have poor fit to the
electron density.
Mol
1
2

Chain
A
B

Length
141
146

Quality of chain

The following table lists non-polymeric compounds that are outliers for geometric or electrondensity-fit criteria:
Mol
4
4
5
5

Type
HEM
HEM
OXY
OXY

Chain
A
B
A
B

Res
143
147
150
150

Geometry
-

Electron density
X
X
X
X

Page 3

Full wwPDB X-ray Structure Validation Report

Entry composition

1HHO

O
i

There are 6 unique types of molecules in this entry. The entry contains 2396 atoms, of which 0
are hydrogen and 0 are deuterium.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate
conformation and the Trace column contains the number of residues modelled with at most 2
atoms.
Molecule 1 is a protein called HEMOGLOBIN A (OXY) (ALPHA CHAIN).

Mol

Chain

Residues

141

Total
1069

Atoms
C
N
O
685 187 194

S
3

ZeroOcc

AltConf

Trace

Molecule 2 is a protein called HEMOGLOBIN A (OXY) (BETA CHAIN).

Mol
2

Chain
B

Residues
146

Total
1123

Atoms
C
N
O
724 195 201

S
3

ZeroOcc

AltConf

Trace

Molecule 3 is PHOSPHATE ION (three-letter code: PO4) (formula: O4 P).

Mol

Chain

Residues

Atoms
Total O P
5
4 1

ZeroOcc

AltConf

Molecule 4 is PROTOPORPHYRIN IX CONTAINING FE (three-letter code: HEM) (for-

Page 4

Full wwPDB X-ray Structure Validation Report

1HHO

mula: C34 H32 FeN4 O4 ).

Mol

Chain

Residues

Total
43
Total
43

Atoms
C Fe
34 1
C Fe
34 1

N
4
N
4

O
4
O
4

ZeroOcc

AltConf

Molecule 5 is OXYGEN MOLECULE (three-letter code: OXY) (formula: O2 ).

Mol

Chain

Residues

Atoms
ZeroOcc AltConf
Total O
0
0
2
2
Continued on next page...

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Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Residues
Atoms
Total O
5
B
1
2
2

ZeroOcc

AltConf

ZeroOcc

AltConf

Molecule 6 is water.

Mol

Chain

Residues

48

61

Atoms
Total O
48
48
Total O
61
61

1HHO

E121
F122
T123
P124
P125
V126
Q127
A128
A129
Y130
Q131
K132
V133
V134
A135
G136
V137
A138
N139
A140
L141
A142
H143
K144
Y145
H146

K61
A62
H63
G64
K65
K66
V67
L68
G69
A70
F71
S72
D73
G74
L75
A76
H77
L78
D79
N80
L81
K82
G83
T84
F85
A86
T87
L88
S89
E90
L91
H92
C93
D94
K95
L96
H97
V98
D99
P100
E101
N102
F103
R104
L105
L106
G107
N108
V109
L110
V111
C112
V113
L114
A115
H116
H117
F118
G119
K120

V1
H2
L3
T4
P5
E6
E7
K8
S9
A10
V11
T12
A13
L14
W15
G16
K17
V18
N19
V20
D21
E22
V23
G24
G25
E26
A27
L28
G29
R30
L31
L32
V33
V34
Y35
P36
W37
T38
Q39
R40
F41
F42
E43
S44
F45
G46
D47
L48
S49
T50
P51
D52
A53
V54
M55
G56
N57
P58
K59
V60

V121
H122
A123
S124
L125
D126
K127
F128
L129
A130
S131
V132
S133
T134
V135
L136
T137
S138
K139
Y140
R141

K61
V62
A63
D64
A65
L66
T67
N68
A69
V70
A71
H72
V73
D74
D75
M76
P77
N78
A79
L80
S81
A82
L83
S84
D85
L86
H87
A88
H89
K90
L91
R92
V93
D94
P95
V96
N97
F98
K99
L100
L101
S102
H103
C104
L105
L106
V107
T108
L109
A110
A111
H112
L113
P114
A115
E116
F117
T118
P119
A120

V1
L2
S3
P4
A5
D6
K7
T8
N9
V10
K11
A12
A13
W14
G15
K16
V17
G18
A19
H20
A21
G22
E23
Y24
G25
A26
E27
A28
L29
E30
R31
M32
F33
L34
S35
F36
P37
T38
T39
K40
T41
Y42
F43
P44
H45
F46
D47
L48
S49
H50
G51
S52
A53
Q54
V55
K56
G57
H58
G59
K60

Page 6

Full wwPDB X-ray Structure Validation Report

Residue-property plots

Molecule 1: HEMOGLOBIN A (OXY) (ALPHA CHAIN)

Chain A:

Molecule 2: HEMOGLOBIN A (OXY) (BETA CHAIN)

Chain B:

1HHO

These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a
chain summarises the proportions of errors displayed in the second graphic. The second graphic
shows the sequence view annotated by issues in geometry and electron density. Residues are colorcoded according to the number of geometric quality criteria for which they contain at least one
outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates
a poor fit to the electron density (RSRZ > 2). Stretches of 2 or more consecutive residues without
any outlier are shown as a green connector. Residues present in the sample, but not in the model,
are shown in grey.

Page 7

Full wwPDB X-ray Structure Validation Report

Data and refinement statistics


Property
Space group
Cell constants
a, b, c, , ,
Resolution (
A)
% Data completeness
(in resolution range)
Rmerge
Rsym
< I/(I) > 1
Refinement program
R, Rf ree

Rf ree test set


Wilson B-factor (
A2 )
Anisotropy
Bulk solvent ksol (e/
A3 ), Bsol (
A2 )
Estimated twinning fraction
L-test for twinning
Outliers
Fo ,Fc correlation
Total number of atoms
Average B, all atoms (
A2 )

1HHO

O
i

Value
P 41 21 2

53.70A 53.70
A 193.80
A

90.00
90.00
90.00
(Not available) 2.10
9.49
2.10
(Not available) ((Not available)-2.10)
98.9 (9.49-2.10)
(Not available)
(Not available)
1.21 (at 2.11
A)
unknown
0.223 , (Not available)
0.235 , (Not available)
No test flags present.
35.3
0.043
0.54 , 92.9
No twinning to report.
< |L| > = 0.48, < L2 > = 0.32
1 of 17050 reflections (0.006%)
0.46
2396
39.0

Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
Depositor
DCC
DCC
Xtriage
Xtriage
EDS
Xtriage
Xtriage
Xtriage
EDS
wwPDB-VP
wwPDB-VP

Xtriages analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 6.23% of the height of the origin peak. No significant pseudotranslation is detected.

Intensities estimated from amplitudes.

Page 8

Full wwPDB X-ray Structure Validation Report

Model quality

5.1

1HHO

Standard geometry

O
i

Bond lengths and bond angles in the following residue types are not validated in this section:
HEM, PO4, OXY
The Z score for a bond length (or angle) is the number of standard deviations the observed value
is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an
outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or
angles).
Mol

Chain

1
2
All

A
B
All

Bond lengths
RMSZ #|Z| >5
1.06
0/1097
1.02
0/1153
1.04
0/2250

Bond angles
RMSZ
#|Z| >5
1.74
12/1491 (0.8%)
1.67
15/1566 (1.0%)
1.71
27/3057 (0.9%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying
if the center is modelled as a planar moiety or with the opposite hand. A planarity outlier is
detected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms
of a sidechain that are expected to be planar.
Mol
1
2
All

Chain
A
B
All

#Chirality outliers
0
0
0

#Planarity outliers
1
1
2

There are no bond length outliers.


All (27) bond angle outliers are listed below:
Mol
1
1
1
1
2
2
1
1
1
2
2
2

Chain
A
A
A
A
B
B
A
A
A
B
B
B

Res
31
92
92
31
145
12
141
42
141
1
12
145

Type
ARG
ARG
ARG
ARG
TYR
THR
ARG
TYR
ARG
VAL
THR
TYR

Atoms
NE-CZ-NH1
NE-CZ-NH2
NE-CZ-NH1
NE-CZ-NH2
CB-CG-CD1
N-CA-CB
NE-CZ-NH1
CB-CG-CD1
NE-CZ-NH2
CA-CB-CG1
CA-CB-CG2
CB-CG-CD2

Z
16.70
-13.09
12.64
-10.74
-9.90
-9.10
9.07
-7.48
-7.46
-7.18
7.08
6.88

Observed(o ) Ideal(o )
128.65
120.30
113.75
120.30
126.62
120.30
114.93
120.30
115.06
121.00
93.01
110.30
124.84
120.30
116.51
121.00
116.57
120.30
100.13
110.90
122.30
112.40
125.13
121.00
Continued on next page...

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Full wwPDB X-ray Structure Validation Report

Continued from
Mol Chain
2
B
2
B
1
A
1
A
2
B
2
B
2
B
2
B
2
B
1
A
1
A
1
A
2
B
2
B
2
B

previous page...
Res Type
Atoms
30
ARG NE-CZ-NH2
40
ARG NE-CZ-NH1
89
HIS
O-C-N
28
ALA
N-CA-CB
55
MET
CG-SD-CE
109 VAL CA-CB-CG2
104 ARG NE-CZ-NH2
130 TYR CB-CG-CD2
47
ASP CB-CG-OD2
7
LYS
CB-CA-C
138 SER
C-N-CA
72
HIS
CA-CB-CG
2
HIS
O-C-N
47
ASP CB-CG-OD1
21
ASP CB-CG-OD1

Z
-6.86
6.83
6.34
-6.34
-5.79
5.79
-5.54
-5.50
5.38
5.30
-5.29
5.25
5.14
-5.02
5.01

Observed(o )
116.87
123.71
132.85
101.22
90.94
119.58
117.53
117.70
123.14
121.01
108.48
122.52
130.93
113.78
122.81

1HHO

Ideal(o )
120.30
120.30
122.70
110.10
100.20
110.90
120.30
121.00
118.30
110.40
121.70
113.60
122.70
118.30
118.30

There are no chirality outliers.


All (2) planarity outliers are listed below:
Mol
1
2

5.2

Chain
A
B

Res
141
145

Type
ARG
TYR

Close contacts

Group
Sidechain
Sidechain

O
i

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms
and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogens
added by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit,
and the number in parentheses is this value normalized per 1000 atoms of the molecule in the
chain. The Symm-Clashes column gives symmetry related clashes, in the same way as for the
Clashes column.
Mol
1
2
3
4
4
5
5
6

Chain
A
B
A
A
B
A
B
A

Non-H
1069
1123
5
43
43
2
2
48

H(model)
0
0
0
0
0
0
0
0

H(added)
1073
1118
0
30
30
0
0
0

Clashes Symm-Clashes
47
1
82
1
0
0
5
0
4
0
0
0
0
0
15
2
Continued on next page...

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Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Non-H H(model)
6
B
61
0
All
All
2396
0

H(added)
0
2251

Clashes
22
131

1HHO

Symm-Clashes
0
2

Clashscore is defined as the number of clashes calculated for the entry per 1000 atoms (including
hydrogens) of the entry. The overall clashscore for this entry is 29.
All (131) close contacts within the same asymmetric unit are listed below.
Atom-1
2:B:126:VAL:HB
1:A:37:PRO:HB3
1:A:24:TYR:HB3
2:B:95:LYS:HE2
1:A:30:GLU:OE1
1:A:64:ASP:OD1
1:A:109:LEU:CD1
2:B:27:ALA:HB2
2:B:97:HIS:HD2
1:A:103:HIS:HD2
1:A:109:LEU:HD11
2:B:144:LYS:HB2
2:B:144:LYS:CB
2:B:95:LYS:CE
2:B:123:THR:N
2:B:37:TRP:HE1
2:B:75:LEU:CD1
1:A:108:THR:CG2
2:B:68:LEU:HD13
2:B:68:LEU:HB3
1:A:108:THR:HG21
1:A:92:ARG:HH11
2:B:43:GLU:CD
2:B:73:ASP:O
1:A:4:PRO:HA
2:B:104:ARG:NH2
2:B:100:PRO:HD3
1:A:23:GLU:OE2
2:B:1:VAL:HG21
2:B:43:GLU:CG
2:B:93:CYS:SG
2:B:58:PRO:HA
2:B:41:PHE:CE2
1:A:46:PHE:HB3

Atom-2
6:B:207:HOH:O
6:A:155:HOH:O
6:A:160:HOH:O
6:B:182:HOH:O
6:A:163:HOH:O
6:A:180:HOH:O
6:A:161:HOH:O
2:B:113:VAL:HG21
6:B:151:HOH:O
6:A:154:HOH:O
6:A:161:HOH:O
6:B:181:HOH:O
6:B:181:HOH:O
6:B:182:HOH:O
6:B:207:HOH:O
2:B:102:ASN:HD21
2:B:133:VAL:HG11
6:A:160:HOH:O
6:B:196:HOH:O
6:B:196:HOH:O
6:A:160:HOH:O
1:A:92:ARG:HG3
6:B:174:HOH:O
2:B:77:HIS:HB2
1:A:7:LYS:HD3
6:B:204:HOH:O
2:B:145:TYR:CE2
6:A:158:HOH:O
2:B:78:LEU:HB3
6:B:174:HOH:O
2:B:145:TYR:CE2
2:B:61:LYS:HG2
2:B:98:VAL:HG22
1:A:48:LEU:HD13

) Clash(
Distance(A
A)
1.32
1.29
1.15
1.25
1.49
1.12
1.67
0.94
1.85
0.92
1.91
0.86
2.23
0.86
1.59
0.85
1.61
0.83
1.61
0.82
1.81
0.80
1.81
0.79
2.31
0.79
2.26
0.78
2.16
0.78
1.32
0.77
2.17
0.75
2.35
0.74
1.87
0.74
1.89
0.72
1.90
0.72
1.56
0.70
2.31
0.68
1.93
0.68
1.75
0.67
2.27
0.67
2.30
0.67
2.12
0.66
1.77
0.65
2.44
0.64
2.90
0.64
1.78
0.63
2.33
0.63
1.80
0.62
Continued on next page...

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Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Atom-1
Atom-2
2:B:101:GLU:O
2:B:105:LEU:HG
1:A:35:SER:HB3
2:B:131:GLN:HG3
4:B:147:HEM:HHA 4:B:147:HEM:HBD1
1:A:73:VAL:HG23
1:A:76:MET:HE3
1:A:37:PRO:CB
6:A:155:HOH:O
2:B:14:LEU:HD11
2:B:122:PHE:HD1
2:B:144:LYS:HG3
6:B:202:HOH:O
2:B:122:PHE:HA
6:B:207:HOH:O
1:A:89:HIS:HE1
1:A:139:LYS:HD3
2:B:75:LEU:HD12
2:B:133:VAL:HG11
1:A:3:SER:HB2
1:A:4:PRO:HD2
2:B:1:VAL:CG1
2:B:81:LEU:HD22
1:A:85:ASP:O
1:A:89:HIS:HB2
2:B:28:LEU:O
2:B:32:LEU:HG
2:B:98:VAL:HG11
4:B:147:HEM:HAC
1:A:10:VAL:HG22
1:A:125:LEU:HD12
1:A:42:TYR:C
1:A:44:PRO:HD3
2:B:129:ALA:O
2:B:133:VAL:HG23
2:B:22:GLU:CG
6:B:172:HOH:O
2:B:37:TRP:HE1
2:B:102:ASN:ND2
1:A:17:VAL:CG2
1:A:113:LEU:HD11
1:A:109:LEU:HD13
6:A:161:HOH:O
2:B:66:LYS:CE
2:B:66:LYS:HA
2:B:32:LEU:HB3
2:B:39:GLN:HG3
1:A:17:VAL:HG23
1:A:113:LEU:HD11
2:B:66:LYS:HE3
2:B:66:LYS:HA
2:B:92:HIS:HA
2:B:96:LEU:HD12
2:B:105:LEU:O
2:B:109:VAL:HG13
2:B:98:VAL:CG1
4:B:147:HEM:HAC
2:B:140:ALA:O
6:B:210:HOH:O
2:B:31:LEU:HD22
2:B:106:LEU:HD13
2:B:109:VAL:O
2:B:113:VAL:HG23
2:B:100:PRO:HA
2:B:103:PHE:CD2
2:B:104:ARG:CZ
6:B:204:HOH:O
4:A:143:HEM:HAD1
6:A:189:HOH:O
2:B:21:ASP:HA
2:B:65:LYS:HD2
2:B:24:GLY:HA3
2:B:64:GLY:O
1:A:7:LYS:HD2
6:A:153:HOH:O
2:B:22:GLU:CB
6:B:172:HOH:O
1:A:138:SER:HA
1:A:141:ARG:HD2
2:B:78:LEU:HA
2:B:81:LEU:HD13
1:A:83:LEU:HD21
4:A:143:HEM:HBA2

Distance(
A) Clash(
A)
1.98
0.62
1.81
0.62
1.80
0.62
1.81
0.62
1.98
0.62
1.65
0.60
2.00
0.60
2.02
0.60
1.66
0.59
1.85
0.59
1.85
0.58
2.33
0.58
2.04
0.58
2.05
0.57
1.86
0.57
1.87
0.56
2.25
0.56
2.05
0.56
2.53
0.56
2.02
0.56
2.36
0.55
1.99
0.55
2.37
0.55
1.87
0.55
1.88
0.55
1.89
0.55
1.89
0.54
2.07
0.54
2.36
0.54
2.18
0.54
1.90
0.54
2.07
0.54
2.43
0.54
2.56
0.52
2.08
0.52
1.90
0.52
2.10
0.52
2.08
0.52
2.59
0.51
1.93
0.50
1.93
0.50
1.91
0.50
Continued on next page...

1HHO

Page 12

Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Atom-1
Atom-2
2:B:58:PRO:O
2:B:62:ALA:HB2
1:A:92:ARG:NH1
1:A:92:ARG:HG3
1:A:37:PRO:CG
6:A:155:HOH:O
1:A:31:ARG:HD3
2:B:127:GLN:OE1
2:B:75:LEU:HD13
2:B:133:VAL:HG11
2:B:17:LYS:HE2
6:B:171:HOH:O
2:B:4:THR:HB
2:B:5:PRO:HD2
2:B:58:PRO:HA
2:B:61:LYS:CG
1:A:76:MET:HE1
1:A:128:PHE:CE1
2:B:8:LYS:O
2:B:12:THR:HB
2:B:128:ALA:O
2:B:132:LYS:HG3
2:B:144:LYS:CG
6:B:181:HOH:O
2:B:59:LYS:O
2:B:62:ALA:HB3
1:A:73:VAL:HG23
1:A:76:MET:CE
4:A:143:HEM:HBB2 4:A:143:HEM:HMB1
1:A:46:PHE:CB
1:A:48:LEU:HD13
1:A:66:LEU:O
1:A:70:VAL:HG23
2:B:43:GLU:HG2
6:B:174:HOH:O
2:B:24:GLY:HA3
2:B:68:LEU:HG
1:A:46:PHE:HB3
1:A:48:LEU:CD1
1:A:76:MET:N
1:A:77:PRO:HD2
1:A:80:LEU:HD12
1:A:135:VAL:HG11
2:B:81:LEU:HD12
2:B:81:LEU:HA
1:A:89:HIS:HE1
1:A:139:LYS:CD
2:B:122:PHE:C
6:B:207:HOH:O
2:B:1:VAL:HG11
2:B:81:LEU:HD22
2:B:32:LEU:HB3
2:B:39:GLN:CG
2:B:1:VAL:HG23
2:B:2:HIS:N
2:B:24:GLY:CA
2:B:68:LEU:HG
1:A:83:LEU:HD21
4:A:143:HEM:CBA
2:B:99:ASP:HA
2:B:100:PRO:HD2
1:A:89:HIS:CE1
1:A:139:LYS:HD3
2:B:93:CYS:SG
2:B:145:TYR:CD2
1:A:83:LEU:CD2
4:A:143:HEM:HBA2
2:B:4:THR:OG1
2:B:6:GLU:HG3
2:B:57:ASN:HA
2:B:58:PRO:HD3
2:B:1:VAL:HG11
2:B:78:LEU:HB3
2:B:63:HIS:O
2:B:66:LYS:HB2
2:B:27:ALA:CB
2:B:113:VAL:HG21
1:A:121:VAL:O
1:A:125:LEU:HB2
2:B:144:LYS:HD3
2:B:144:LYS:HA
2:B:48:LEU:HB3
2:B:54:VAL:HG22

Distance(
A) Clash(
A)
2.12
0.50
2.26
0.49
2.51
0.48
2.12
0.48
1.96
0.48
2.12
0.48
1.95
0.48
2.43
0.48
2.49
0.48
2.14
0.48
2.13
0.47
2.60
0.47
2.15
0.47
2.43
0.47
1.96
0.47
2.45
0.47
2.14
0.47
2.10
0.46
1.97
0.46
2.44
0.46
2.29
0.46
1.98
0.46
1.64
0.46
2.27
0.46
2.51
0.46
1.98
0.45
2.46
0.45
2.32
0.45
2.47
0.45
2.46
0.45
1.46
0.45
2.49
0.44
3.01
0.44
2.48
0.44
2.18
0.44
1.64
0.43
1.99
0.43
2.19
0.43
2.41
0.43
2.19
0.43
1.47
0.42
2.01
0.42
Continued on next page...

1HHO

Page 13

Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Atom-1
Atom-2
2:B:95:LYS:HA
2:B:95:LYS:HD3
2:B:1:VAL:H1
2:B:1:VAL:HG12
1:A:89:HIS:HE1
1:A:139:LYS:NZ
1:A:89:HIS:CE1
1:A:139:LYS:NZ
1:A:66:LEU:HD23
1:A:66:LEU:HA
2:B:58:PRO:HB3
2:B:61:LYS:HE2
2:B:89:SER:OG
2:B:144:LYS:HB2
2:B:135:ALA:O
2:B:139:ASN:ND2
2:B:14:LEU:HD11
2:B:122:PHE:CD1
1:A:42:TYR:O
1:A:44:PRO:HD3
1:A:81:SER:O
1:A:84:SER:HB2
2:B:1:VAL:HG11
2:B:78:LEU:O
4:B:147:HEM:HBB2 4:B:147:HEM:HMB2

Distance(
A)
1.66
1.38
2.17
2.88
1.85
2.00
2.20
2.53
2.51
2.21
2.21
2.21
2.03

1HHO

Clash(
A)
0.42
0.42
0.42
0.42
0.42
0.42
0.42
0.41
0.41
0.41
0.41
0.41
0.40

All (2) symmetry-related close contacts are listed below. The label for Atom-2 includes the symmetry operator and encoded unit-cell translations to be applied.
Atom-1
1:A:14:TRP:CD1
2:B:93:CYS:C

5.3
5.3.1

Atom-2
6:A:196:HOH:O[5 655]
6:A:166:HOH:O[7 555]

Torsion angles

)
Distance(A
2.06
2.15

)
Clash(A
0.14
0.05

Protein backbone i

In the following table, the Percentiles column shows the percent Ramachandran outliers of the
chain as a percentile score with respect to all X-ray entries followed by that with respect to entries
of similar resolution. The Analysed column shows the number of residues for which the backbone
conformation was analysed, and the total number of residues.
Mol

Chain

Analysed

Favoured

Allowed

Outliers

139/141 (99%)

128 (92%)

10 (7%)

1 (1%)

30

23

144/146 (99%)

132 (92%)

8 (6%)

4 (3%)

All

All

283/287 (99%)

260 (92%)

18 (6%)

5 (2%)

13

All (5) Ramachandran outliers are listed below:


Mol
1
2

Chain Res
Type
A
72
HIS
B
3
LEU
Continued on next page...

Percentiles

Page 14

Full wwPDB X-ray Structure Validation Report

Continued from
Mol Chain
2
B
2
B
2
B

5.3.2

1HHO

previous page...
Res
Type
77
HIS
40
ARG
100
PRO

Protein sidechains i

In the following table, the Percentiles column shows the percent sidechain outliers of the chain
as a percentile score with respect to all X-ray entries followed by that with respect to entries of
similar resolution. The Analysed column shows the number of residues for which the sidechain
conformation was analysed, and the total number of residues.
Mol

Chain

Analysed

Rotameric

Outliers

Percentiles

113/113 (100%)

102 (90%)

11 (10%)

12

118/118 (100%)

102 (86%)

16 (14%)

All

All

231/231 (100%)

204 (88%)

27 (12%)

All (27) residues with a non-rotameric sidechain are listed below:


Mol
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
2

Chain Res
Type
A
7
LYS
A
38
THR
A
41
THR
A
48
LEU
A
56
LYS
A
86
LEU
A
92
ARG
A
96
VAL
A
105
LEU
A
109
LEU
A
125
LEU
B
3
LEU
B
9
SER
B
20
VAL
B
26
GLU
B
28
LEU
B
40
ARG
B
50
THR
B
66
LYS
B
73
ASP
B
77
HIS
B
81
LEU
Continued on next page...

Page 15

Full wwPDB X-ray Structure Validation Report

Continued from
Mol Chain
2
B
2
B
2
B
2
B
2
B

1HHO

previous page...
Res
Type
94
ASP
110
LEU
134
VAL
144
LYS
146
HIS

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (6) such
sidechains are listed below:
Mol
1
1
1
1
2
2

5.3.3

Chain
A
A
A
A
B
B

Res
9
89
97
103
102
108

Type
ASN
HIS
ASN
HIS
ASN
ASN

RNA i

There are no RNA chains in this entry.

5.4

Non-standard residues in protein, DNA, RNA chains

O
i

There are no non-standard protein/DNA/RNA residues in this entry.

5.5

Carbohydrates

O
i

There are no carbohydrates in this entry.

5.6

Ligand geometry

O
i

5 ligands are modelled in this entry.


In the following table, the Counts columns list the number of bonds (or angles) for which Mogul
statistics could be retrieved, the number of bonds (or angles) that are observed in the model and
the number of bonds (or angles) that are defined in the chemical component dictionary. The Link
column lists molecule types, if any, to which the group is linked. The Z score for a bond length
(or angle) is the number of standard deviations the observed value is removed from the expected
value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection. RMSZ is
the root-mean-square of all Z scores of the bond lengths (or angles).

Page 16

Full wwPDB X-ray Structure Validation Report

Mol

Type

Chain

Res

Link

3
4
5
4
5

PO4
HEM
OXY
HEM
OXY

A
A
A
B
B

142
143
150
147
150

1,5
4
2,5
4

Bond lengths
Counts RMSZ #|Z| > 2
4,4,4
1.45
0
49,50,50
2.11
13 (26%)
1,1,1
0.55
0
49,50,50
2.83
11 (22%)
1,1,1
0.75
0

1HHO

Bond angles
Counts RMSZ #|Z| > 2
6,6,6
0.36
0
46,82,82
1.71
11 (23%)
0,0,0
0.00
46,82,82
1.92
12 (26%)
0,0,0
0.00
-

In the following table, the Chirals column lists the number of chiral outliers, the number of chiral
centers analysed, the number of these observed in the model and the number defined in the chemical
component dictionary. Similar counts are reported in the Torsion and Rings columns. - means
no outliers of that kind were identified.
Mol
3
4
5
4
5

Type
PO4
HEM
OXY
HEM
OXY

Chain
A
A
A
B
B

Res
142
143
150
147
150

Link
1,5
4
2,5
4

Chirals
-

Torsions
0/0/0/0
0/14/114/114
0/0/0/0
0/14/114/114
0/0/0/0

Rings
0/0/0/0
0/0/8/8
0/0/0/0
0/0/8/8
0/0/0/0

All (24) bond length outliers are listed below:


Mol
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4

Chain
B
A
A
B
B
B
B
A
A
A
A
A
A
B
B
B
B
A
A
B
B

Res
147
143
143
147
147
147
147
143
143
143
143
143
143
147
147
147
147
143
143
147
147

Type
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM

Atoms
C2B-C1B
C2D-C1D
C3D-C2D
C3D-C4D
C3D-C2D
C3C-C2C
C4A-C3A
C3C-C2C
CHA-C4D
C2B-C1B
C3B-CAB
C3B-C2B
C3C-CAC
C3B-C2B
C3B-CAB
C3C-CAC
CHB-C1B
C4C-NC
FE-NA
FE-NC
C3B-C4B

Z
-14.55
-6.14
-5.91
-5.59
-5.33
-4.91
4.28
-4.22
4.05
3.97
3.95
-3.50
3.31
-3.30
3.08
2.95
2.87
2.51
2.25
2.23
-2.21

Observed(
A) Ideal(
A)
1.40
1.44
1.43
1.44
1.33
1.43
1.43
1.44
1.34
1.43
1.35
1.43
1.45
1.40
1.36
1.43
1.41
1.35
1.45
1.44
1.52
1.40
1.37
1.43
1.50
1.40
1.38
1.43
1.50
1.40
1.49
1.40
1.39
1.35
1.41
1.38
2.02
1.92
2.06
1.97
1.41
1.44
Continued on next page...

Page 17

Full wwPDB X-ray Structure Validation Report

Continued from
Mol Chain
4
A
4
A
4
A

previous page...
Res Type
Atoms
143 HEM CHC-C1C
143 HEM O2A-CGA
143 HEM CBB-CAB

Z
2.13
-2.08
2.00

Observed(
A)
1.40
1.23
1.40

1HHO

Ideal(
A)
1.36
1.30
1.28

All (23) bond angle outliers are listed below:


Mol
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4

Chain
B
A
A
B
B
A
B
B
A
A
B
B
A
B
B
B
B
A
A
A
A
B
A

Res
147
143
143
147
147
143
147
147
143
143
147
147
143
147
147
147
147
143
143
143
143
147
143

Type
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM
HEM

Atoms
C4A-CHB-C1B
CMA-C3A-C4A
CBA-CAA-C2A
C3B-C4B-NB
CHC-C4B-NB
C4A-CHB-C1B
CMA-C3A-C4A
CBA-CAA-C2A
CMA-C3A-C2A
C3A-C4A-NA
C3A-C4A-NA
CBD-CAD-C3D
CAA-CBA-CGA
O1D-CGD-CBD
CMB-C2B-C3B
C2D-C1D-ND
CHA-C4D-ND
C2D-C1D-ND
CAD-CBD-CGD
CAD-C3D-C4D
C1B-NB-C4B
C4A-NA-C1A
C4C-NC-C1C

There are no chirality outliers.


There are no torsion outliers.
There are no ring outliers.

5.7

Other polymers

O
i

There are no such residues in this entry.

Z
-4.46
-4.42
4.32
-4.26
4.22
-3.85
-3.55
3.49
3.22
3.21
2.89
-2.85
-2.41
-2.40
2.30
-2.25
2.21
-2.21
-2.15
2.11
-2.08
-2.06
-2.02

Observed(o )
121.61
121.83
120.31
110.95
128.09
122.40
123.17
118.84
131.02
111.83
111.59
108.16
105.74
114.78
131.57
110.28
127.34
110.32
106.78
128.32
103.03
104.05
103.44

Ideal(o )
127.47
128.62
112.69
114.00
124.58
127.47
128.62
112.69
124.94
109.41
109.41
114.37
113.47
123.03
126.16
112.93
124.31
112.93
113.48
124.53
105.16
106.76
105.53

Page 18

5.8

Full wwPDB X-ray Structure Validation Report

Polymer linkage issues

There are no chain breaks in this entry.

1HHO

Page 19

Full wwPDB X-ray Structure Validation Report

Fit of model and data

6.1

1HHO

Protein, DNA and RNA chains

O
i

In the following table, the column labelled #RSRZ> 2 contains the number (and percentage)
of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative to
all X-ray entries and entries of similar resolution. The OWAB column contains the minimum,
median, 95th percentile and maximum values of the occupancy-weighted average B-factor per
residue. The column labelled Q< 0.9 lists the number of (and percentage) of residues with an
average occupancy less than 0.9.
2 )
OWAB(A

Q<0.9

14, 34, 55, 82

146 (100%) 0

17, 42, 69, 81

287 (100%) 0

14, 38, 67, 82

Mol

Chain

Analysed

<RSRZ>

141/141 (100%)

13.19

141 (100%) 0

146/146 (100%)

10.83

All

All

287/287 (100%)

11.99

All (287) RSRZ outliers are listed below:


Mol
1
2
2
2
2
2
2
1
1
1
2
1
2
2
2
1
2
1
1
2
1
2
1
1

Chain Res Type RSRZ


A
55
VAL
23.3
B
32
LEU
22.6
B
113 VAL
21.9
B
15
TRP
21.8
B
125 PRO
21.7
B
103 PHE
21.4
B
105 LEU
21.4
A
88
ALA
21.1
A
13
ALA
21.1
A
38
THR
20.9
B
133 VAL
20.9
A
14
TRP
20.6
B
112 CYS
20.5
B
130 TYR
20.0
B
115 ALA
19.7
A
137 THR
19.6
B
108 ASN
19.6
A
138 SER
19.2
A
22
GLY
18.9
B
11
VAL
18.8
A
62
VAL
18.7
B
16
GLY
18.3
A
2
LEU
18.3
A
34
LEU
18.3
Continued on next page...

#RSRZ>2

Page 20

Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Res Type RSRZ
1
A
43
PHE
18.2
1
A
104 CYS
18.1
1
A
98
PHE
18.0
2
B
99
ASP
17.7
1
A
83
LEU
17.7
1
A
1
VAL
17.5
2
B
60
VAL
17.5
1
A
29
LEU
17.4
1
A
93
VAL
17.4
2
B
111 VAL
17.4
2
B
4
THR
17.3
1
A
9
ASN
17.3
1
A
48
LEU
17.2
1
A
53
ALA
17.1
2
B
25
GLY
17.0
1
A
77
PRO
17.0
1
A
49
SER
16.9
1
A
33
PHE
16.9
1
A
72
HIS
16.8
1
A
32
MET
16.8
1
A
46
PHE
16.5
1
A
68
ASN
16.5
1
A
136 LEU
16.4
1
A
57
GLY
16.4
2
B
85
PHE
16.4
1
A
15
GLY
16.3
1
A
71
ALA
16.2
1
A
75
ASP
16.2
1
A
66
LEU
16.0
1
A
82
ALA
15.9
1
A
140 TYR
15.9
1
A
67
THR
15.7
1
A
8
THR
15.7
1
A
10
VAL
15.6
2
B
129 ALA
15.6
1
A
41
THR
15.5
1
A
105 LEU
15.5
2
B
124 PRO
15.5
1
A
70
VAL
15.4
2
B
18
VAL
15.3
1
A
59
GLY
15.2
1
A
39
THR
15.2
Continued on next page...

1HHO

Page 21

Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Res Type RSRZ
2
B
96
LEU
15.1
1
A
80
LEU
15.1
1
A
132 VAL
15.0
1
A
73
VAL
14.9
2
B
27
ALA
14.9
1
A
26
ALA
14.8
1
A
129 LEU
14.7
2
B
33
VAL
14.6
1
A
134 THR
14.6
1
A
28
ALA
14.5
1
A
110 ALA
14.5
1
A
102 SER
14.4
2
B
107 GLY
14.4
1
A
100 LEU
14.4
1
A
35
SER
14.3
1
A
37
PRO
14.3
2
B
14
LEU
14.3
1
A
56
LYS
14.3
1
A
139
LYS
14.2
1
A
3
SER
14.0
1
A
101 LEU
13.9
2
B
93
CYS
13.9
1
A
52
SER
13.9
2
B
13
ALA
13.8
1
A
63
ALA
13.8
1
A
106 LEU
13.8
2
B
92
HIS
13.7
2
B
141 LEU
13.4
1
A
107 VAL
13.4
2
B
1
VAL
13.4
1
A
122
HIS
13.4
2
B
23
VAL
13.3
2
B
67
VAL
13.3
1
A
5
ALA
13.3
2
B
122 PHE
13.3
1
A
133 SER
13.3
2
B
36
PRO
13.2
1
A
6
ASP
13.1
2
B
91
LEU
13.1
2
B
31
LEU
13.0
1
A
141 ARG
13.0
1
A
4
PRO
13.0
Continued on next page...

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Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Res Type RSRZ
1
A
135 VAL
12.9
1
A
69
ALA
12.9
1
A
128 PHE
12.9
1
A
103
HIS
12.8
1
A
54
GLN
12.8
1
A
40
LYS
12.8
1
A
50
HIS
12.6
1
A
74
ASP
12.6
1
A
36
PHE
12.6
2
B
100 PRO
12.5
1
A
51
GLY
12.4
2
B
104 ARG
12.4
1
A
123 ALA
12.3
1
A
19
ALA
12.3
1
A
130 ALA
12.3
1
A
85
ASP
12.3
1
A
45
HIS
12.2
2
B
128 ALA
12.2
2
B
63
HIS
12.1
1
A
86
LEU
12.1
1
A
79
ALA
12.1
2
B
101 GLU
12.1
1
A
23
GLU
12.0
1
A
12
ALA
12.0
1
A
118 THR
12.0
2
B
78
LEU
12.0
2
B
83
GLY
11.9
1
A
24
TYR
11.8
1
A
87
HIS
11.8
1
A
25
GLY
11.8
2
B
10
ALA
11.8
2
B
3
LEU
11.8
2
B
28
LEU
11.7
2
B
51
PRO
11.7
2
B
49
SER
11.7
1
A
76
MET
11.6
2
B
70
ALA
11.6
2
B
44
SER
11.5
1
A
111 ALA
11.5
1
A
30
GLU
11.5
2
B
119 GLY
11.5
1
A
58
HIS
11.3
Continued on next page...

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Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Res Type RSRZ
2
B
95
LYS
11.3
1
A
11
LYS
11.2
2
B
81
LEU
11.2
2
B
134 VAL
11.2
1
A
124 SER
11.2
2
B
109 VAL
11.2
1
A
97
ASN
11.1
1
A
21
ALA
11.0
1
A
61
LYS
11.0
2
B
145 TYR
11.0
1
A
18
GLY
11.0
1
A
121 VAL
10.9
1
A
64
ASP
10.9
2
B
116
HIS
10.8
1
A
91
LEU
10.8
1
A
20
HIS
10.8
2
B
5
PRO
10.8
1
A
65
ALA
10.7
2
B
114 LEU
10.6
2
B
98
VAL
10.6
1
A
126 ASP
10.5
2
B
30
ARG
10.5
2
B
37
TRP
10.5
2
B
54
VAL
10.5
2
B
140 ALA
10.5
2
B
53
ALA
10.4
2
B
20
VAL
10.3
1
A
120 ALA
10.2
1
A
109 LEU
10.2
2
B
2
HIS
10.1
1
A
60
LYS
10.1
1
A
47
ASP
10.1
2
B
110 LEU
10.0
2
B
45
PHE
10.0
1
A
96
VAL
9.9
1
A
116 GLU
9.9
2
B
121 GLU
9.9
1
A
108 THR
9.9
1
A
84
SER
9.8
2
B
19
ASN
9.8
1
A
117 PHE
9.8
2
B
35
TYR
9.8
Continued on next page...

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Page 24

Full wwPDB X-ray Structure Validation Report

Continued from previous page...


Mol Chain Res Type RSRZ
2
B
88
LEU
9.8
2
B
62
ALA
9.7
2
B
7
GLU
9.6
2
B
118 PHE
9.6
2
B
90
GLU
9.5
2
B
75
LEU
9.5
2
B
136 GLY
9.4
1
A
125 LEU
9.4
2
B
126 VAL
9.3
2
B
135 ALA
9.3
2
B
68
LEU
9.3
2
B
117
HIS
9.2
1
A
127
LYS
9.2
2
B
42
PHE
9.2
2
B
59
LYS
9.2
2
B
24
GLY
9.1
1
A
16
LYS
9.1
1
A
131 SER
9.0
2
B
97
HIS
8.9
1
A
17
VAL
8.8
2
B
12
THR
8.7
2
B
77
HIS
8.7
2
B
57
ASN
8.7
2
B
47
ASP
8.7
2
B
41
PHE
8.6
2
B
8
LYS
8.6
2
B
34
VAL
8.6
1
A
27
GLU
8.6
2
B
146
HIS
8.6
2
B
29
GLY
8.5
1
A
89
HIS
8.5
2
B
86
ALA
8.5
2
B
72
SER
8.5
2
B
120
LYS
8.4
2
B
132
LYS
8.4
1
A
78
ASN
8.4
2
B
46
GLY
8.4
2
B
127 GLN
8.3
2
B
79
ASP
8.3
1
A
31
ARG
8.2
2
B
131 GLN
8.1
2
B
48
LEU
8.1
Continued on next page...

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Page 25

Full wwPDB X-ray Structure Validation Report

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Mol Chain Res Type RSRZ
2
B
82
LYS
8.1
2
B
102 ASN
8.0
1
A
7
LYS
8.0
1
A
81
SER
8.0
1
A
113 LEU
8.0
2
B
69
GLY
7.9
2
B
84
THR
7.9
2
B
74
GLY
7.8
2
B
17
LYS
7.7
2
B
87
THR
7.7
1
A
90
LYS
7.6
1
A
99
LYS
7.6
2
B
58
PRO
7.6
1
A
44
PRO
7.5
1
A
94
ASP
7.2
2
B
94
ASP
7.1
2
B
138 ALA
6.9
2
B
26
GLU
6.9
2
B
76
ALA
6.8
2
B
9
SER
6.8
2
B
142 ALA
6.8
2
B
80
ASN
6.7
2
B
55
MET
6.6
2
B
89
SER
6.6
1
A
42
TYR
6.6
1
A
114 PRO
6.5
1
A
115 ALA
6.5
1
A
112
HIS
6.5
2
B
6
GLU
6.4
2
B
43
GLU
6.4
1
A
119 PRO
6.4
2
B
143
HIS
6.3
2
B
50
THR
6.3
2
B
52
ASP
6.2
2
B
106 LEU
6.2
2
B
123 THR
6.1
2
B
71
PHE
6.1
2
B
137 VAL
6.1
2
B
139 ASN
6.0
2
B
56
GLY
5.9
2
B
40
ARG
5.9
1
A
95
PRO
5.9
Continued on next page...

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Page 26

Full wwPDB X-ray Structure Validation Report

Continued from
Mol Chain
2
B
2
B
2
B
2
B
2
B
2
B
2
B
1
A
2
B
2
B
2
B

6.2

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previous page...
Res Type RSRZ
64
GLY
5.8
66
LYS
5.7
73
ASP
5.7
22
GLU
5.7
39
GLN
5.7
38
THR
5.6
21
ASP
5.6
92
ARG
4.9
144
LYS
4.3
61
LYS
3.6
65
LYS
3.5

Non-standard residues in protein, DNA, RNA chains

O
i

There are no non-standard protein/DNA/RNA residues in this entry.

6.3

Carbohydrates

O
i

There are no carbohydrates in this entry.

6.4

Ligands

O
i

In the following table, the Atoms column lists the number of modelled atoms in the group and the
number defined in the chemical component dictionary. LLDF column lists the quality of electron
density of the group with respect to its neighbouring residues in protein, DNA or RNA chains.
The B-factors column lists the minimum, median, 95th percentile and maximum values of B factors
of atoms in the group. The column labelled Q< 0.9 lists the number of atoms with occupancy
less than 0.9.
Mol
4
4
5
5
3

6.5

Type
HEM
HEM
OXY
OXY
PO4

Chain
A
B
B
A
A

Res
143
147
150
150
142

Other polymers

Atoms
43/43
43/43
2/2
2/2
5/5

O
i

There are no such residues in this entry.

RSR
0.99
0.73
0.58
0.84
0.30

LLDF
0.48
-0.09
-0.95
-1.19
-3.56

B-factors(
A2 )
13,28,60,76
8,33,75,97
37,37,37,42
17,17,17,33
53,53,62,62

Q<0.9
0
0
0
0
5

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