- PDB-3o0r: Crystal structure of nitric oxide reductase from Pseudomonas aeru... -
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Basic information
Entry
Database: PDB / ID: 3o0r
Title
Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment
Components
(Nitric oxide reductase subunit ...) x 2
(antibody fab fragment ...) x 2
Keywords
IMMUNE SYSTEM/OXIDOREDUCTASE / oxidoreductase / electron transport / heme / iron / membrane / cytoplasmic membrane / IMMUNE SYSTEM-OXIDOREDUCTASE complex
Function / homology
Function and homology information
nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / : / electron transport coupled proton transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / heme binding ...nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / : / electron transport coupled proton transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function
Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c ...Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
: / HEME C / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Nitric oxide reductase subunit C / Nitric oxide reductase subunit B Similarity search - Component
L: antibody fab fragment light chain H: antibody fab fragment heavy chain B: Nitric oxide reductase subunit B C: Nitric oxide reductase subunit C hetero molecules
Redundancy: 11.9 % / Av σ(I) over netI: 5.65 / Number: 530738 / Rmerge(I) obs: 0.101 / Rsym value: 0.094 / Χ2: 2.31 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 44758 / % possible obs: 96.8
Diffraction reflection shell
ID: 1
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
Rmerge(I) obs
Rsym value
Chi squared
Redundancy
7.59
50
96.2
0.039
0.034
2.732
12.7
6.03
7.59
100
0.057
0.044
2.646
13.9
5.27
6.03
100
0.072
0.111
2.945
13
4.79
5.27
99.7
0.072
0.075
2.964
12.7
4.44
4.79
99.4
0.074
0.074
2.743
12.6
4.18
4.44
99.9
0.083
0.117
2.48
12.6
3.97
4.18
99.6
0.101
0.184
2.332
12.6
3.8
3.97
99.6
0.137
0.316
2.25
12.7
3.65
3.8
99.8
0.17
0.489
1.897
12.6
3.53
3.65
99.5
0.195
0.786
2.006
12.7
3.42
3.53
99.5
0.251
2.048
12.6
3.32
3.42
99.6
0.306
2.089
12.6
3.23
3.32
99.4
0.395
2.307
12.3
3.15
3.23
99.2
0.442
1.905
11.8
3.08
3.15
98.5
0.499
2.486
11
3.02
3.08
97.2
0.577
2.035
10.4
2.96
3.02
93.7
0.559
1.795
9.9
2.9
2.96
89.4
0.565
1.843
9.4
2.85
2.9
84.7
0.667
1.711
8.9
2.8
2.85
81.4
0.634
1.968
8.1
Reflection
Resolution: 2.7→41.514 Å / Num. all: 50332 / Num. obs: 50332 / % possible obs: 97.7 % / Redundancy: 4.2 % / Rsym value: 0.094 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Rsym value
Diffraction-ID
% possible all
2.7-2.85
4.2
0.786
1
0.786
1,2,3
99
2.85-3.02
4.2
0.489
1.5
0.489
1,2,3
98.8
3.02-3.23
4.2
0.316
2.4
0.316
1,2,3
98.7
3.23-3.49
4.2
0.184
3.9
0.184
1,2,3
98.2
3.49-3.82
4.2
0.117
6
0.117
1,2,3
98.2
3.82-4.27
4.2
0.074
8.7
0.074
1,2,3
97.7
4.27-4.93
4.2
0.075
7.6
0.075
1,2,3
97.2
4.93-6.04
4.2
0.111
5.3
0.111
1,2,3
96.7
6.04-8.54
4.2
0.044
13
0.044
1,2,3
95.8
8.54-41.514
3.8
0.034
17.8
0.034
1,2,3
87.1
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Phasing
Phasing
Method: molecular replacement
Phasing MR
Rfactor: 56.55 / Model details: Phaser MODE: MR_RNP
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 44644
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
12.52-100
60.5
0.532
514
9.66-12.52
58.8
0.79
652
8.15-9.66
60.4
0.777
782
7.18-8.15
63.9
0.802
913
6.49-7.18
64.9
0.777
990
5.97-6.49
69.3
0.762
1095
5.55-5.97
69.6
0.78
1173
5.21-5.55
64.6
0.815
1254
4.93-5.21
69.7
0.826
1305
4.69-4.93
67.5
0.827
1388
4.48-4.69
66.1
0.851
1443
4.3-4.48
66
0.861
1521
4.14-4.3
68.5
0.845
1560
3.99-4.14
68.4
0.828
1618
3.86-3.99
66.4
0.834
1673
3.74-3.86
72.5
0.826
1728
3.63-3.74
70.6
0.843
1780
3.53-3.63
72.7
0.848
1838
3.44-3.53
75.5
0.841
1886
3.35-3.44
74.8
0.852
1913
3.28-3.35
75.3
0.835
1974
3.2-3.28
76.1
0.821
2008
3.13-3.2
79.8
0.811
2019
3.07-3.13
78.3
0.784
2075
3.01-3.07
80.8
0.776
2088
2.95-3.01
82.7
0.762
2024
2.9-2.95
81.4
0.753
1964
2.8-2.9
82.4
0.619
3466
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Processing
Software
Name
Version
Classification
NB
MOSFLM
datareduction
SCALA
3.3.16
datascaling
PHASER
2.1.4
phasing
DM
6.1
phasing
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.773 / SU ML: 0.241 / SU R Cruickshank DPI: 0.3943 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24739
2559
5.1 %
RANDOM
Rwork
0.18523
-
-
-
obs
0.18828
47669
97.49 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 83.756 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.02 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8060
0
132
172
8364
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
8453
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.913
1.99
11542
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.978
5
1025
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.848
23.204
334
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
22.656
15
1304
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.755
15
36
X-RAY DIFFRACTION
r_chiral_restr
0.133
0.2
1249
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
6532
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.727
1.5
5104
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.384
2
8224
X-RAY DIFFRACTION
r_scbond_it
2.176
3
3349
X-RAY DIFFRACTION
r_scangle_it
3.223
4.5
3318
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.7→2.769 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.432
203
-
Rwork
0.317
3464
-
obs
-
-
98.65 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
4.022
-1.582
0.6565
3.84
0.5083
1.6518
-0.1789
0.583
0.0401
-0.4604
0.2025
-0.2597
-0.2865
0.4701
-0.0236
0.2324
-0.105
0.0181
0.7015
-0.2374
0.4682
34.695
-14.285
-0.651
2
2.9864
1.0082
1.415
4.8921
2.7291
4.4231
-0.2447
0.3013
0.2749
-0.3294
-0.1361
0.4765
-0.4292
-0.4613
0.3809
0.1693
0.0157
-0.0787
0.5965
-0.223
0.5601
13.374
-10.918
0.285
3
1.6772
0.079
-0.0064
3.5851
2.9441
4.5059
-0.0691
-0.1429
0.3375
-0.1966
-0.0998
0.2733
-1.2057
0.1509
0.1689
0.7944
-0.0664
-0.13
0.1955
-0.1421
0.3996
24.49
25.684
35.122
4
1.3444
-0.304
-0.7886
12.4172
6.6405
4.4783
-0.0925
-0.4627
0.0567
2.6045
-0.4242
0.4112
0.8401
-0.1529
0.5166
1.3023
-0.118
0.0593
0.7873
-0.1683
0.5071
19.392
17.076
57.012
5
9.0108
2.216
3.532
4.4433
2.4191
6.2371
-0.1989
0.1099
-0.0535
-0.6441
0.093
0.0177
0.054
-0.1032
0.1059
0.2409
-0.0114
0.0586
0.4355
-0.177
0.4047
26.439
-44.091
-21.721
6
4.017
-1.1193
-0.988
5.0167
1.3283
3.4188
-0.316
-0.4953
-0.6942
-0.2347
0.0612
0.0974
0.6472
0.0852
0.2547
0.2294
-0.018
0.0709
0.674
-0.0984
0.5198
16.238
-47.091
-10.313
7
3.7275
-0.7593
0.5075
4.1058
2.1536
5.337
-0.0387
-0.1305
-0.5268
0.7677
0.0775
-0.0455
0.6023
0.8558
-0.0387
0.4797
0.0342
-0.1252
0.2707
-0.122
0.592
30.425
-2.343
28.27
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
L
1 - 107
2
X-RAY DIFFRACTION
2
H
1 - 112
3
X-RAY DIFFRACTION
3
B
10 - 458
4
X-RAY DIFFRACTION
3
B
801 - 803
5
X-RAY DIFFRACTION
3
C
804
6
X-RAY DIFFRACTION
4
C
5 - 37
7
X-RAY DIFFRACTION
5
L
110 - 213
8
X-RAY DIFFRACTION
6
H
115 - 214
9
X-RAY DIFFRACTION
7
C
38 - 146
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