← Back to search
3wfe

Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment

Method: X-RAY DIFFRACTION Dmax: 135.4 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitric oxide reductase subunit B

OrganismNot specified

UniProt Q59647

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–466 Not recorded antibody fab fragment light chain × 1 antibody fab fragment heavy chain × 1 Nitric oxide reductase subunit C × 1 （Q59646） HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 CYN CYANIDE ION × 2 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；277 K；100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K Resolution 2.49 Å R-free 0.227

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3WFE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3O0R Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2010-07-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–466（466 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% PEG 400, 0.1M sodium citrate, 50mM sodium chloride, 20mM magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.247
3WFB Reduced cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2013-07-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–466（466 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；100 mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Resolution 2.70 Å R-free 0.250
3WFC Reduced and carbonmonoxide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2013-07-18 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–466（466 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 CMO CARBON MONOXIDE × 2 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Resolution 2.50 Å R-free 0.232
3WFD Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2013-07-18 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–466（466 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 AXO (1E)-N-hydroxyethanimine × 1 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Resolution 2.30 Å R-free 0.232
5GUW Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa Deposited 2016-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–466（466 aa） Fragment：Nitric oxide reductase subunit b
Not recorded HEC HEME C × 1 CA CALCIUM ION × 1 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 0.2M CsCl, 12% PEG3350
Resolution 3.20 Å R-free 0.254
5GUW Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa Deposited 2016-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–466（466 aa） Fragment：Nitric oxide reductase subunit b
Not recorded HEC HEME C × 1 CA CALCIUM ION × 1 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 0.2M CsCl, 12% PEG3350
Resolution 3.20 Å R-free 0.254
5GUX Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon Deposited 2016-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–466（466 aa） Fragment：Nitric oxide reductase subunit B
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 XE XENON × 7 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；24% PEG 400, 0.1M SODIUM CITRATE, 50mM SODIUM CHLORIDE, 20mM MAGNESIUM CHLORIDE
Resolution 3.30 Å R-free 0.268

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NORB_PSEAE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–465； UniProt 1–466

Nitric oxide reductase subunit C

OrganismNot specified

UniProt Q59646

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–146 Not recorded antibody fab fragment light chain × 1 antibody fab fragment heavy chain × 1 Nitric oxide reductase subunit B × 1 （Q59647） HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 CYN CYANIDE ION × 2 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；277 K；100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K Resolution 2.49 Å R-free 0.227

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3WFE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3O0R Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2010-07-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–146（146 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% PEG 400, 0.1M sodium citrate, 50mM sodium chloride, 20mM magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.247
3WFB Reduced cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2013-07-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–146（146 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；100 mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Resolution 2.70 Å R-free 0.250
3WFC Reduced and carbonmonoxide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2013-07-18 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–146（146 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 CMO CARBON MONOXIDE × 2 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Resolution 2.50 Å R-free 0.232
3WFD Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment Deposited 2013-07-18 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–146（146 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 AXO (1E)-N-hydroxyethanimine × 1 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K
Resolution 2.30 Å R-free 0.232
5GUW Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa Deposited 2016-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–146（146 aa） Fragment：Nitric oxide reductase subunit c
Mutation：K100N HEC HEME C × 1 CA CALCIUM ION × 1 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 0.2M CsCl, 12% PEG3350
Resolution 3.20 Å R-free 0.254
5GUW Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa Deposited 2016-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–146（146 aa） Fragment：Nitric oxide reductase subunit c
Mutation：K100N HEC HEME C × 1 CA CALCIUM ION × 1 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 0.2M CsCl, 12% PEG3350
Resolution 3.20 Å R-free 0.254
5GUX Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon Deposited 2016-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–146（146 aa） Fragment：UNP residues 5-146, Nitric oxide reductase subunit C
Mutation：K100N HEM PROTOPORPHYRIN IX CONTAINING FE × 2 FE FE (III) ION × 1 O OXYGEN ATOM × 1 XE XENON × 7 10M decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CA CALCIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；277 K；24% PEG 400, 0.1M SODIUM CITRATE, 50mM SODIUM CHLORIDE, 20mM MAGNESIUM CHLORIDE
Resolution 3.30 Å R-free 0.268

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NORC_PSEAE
Isoform —
PDB entities 4
Chains and sequence ranges Author chain C； PDBConstruct 1–146； UniProt 1–146

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3wfe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wfe
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3wfe
Deposition date deposition_date2013-07-18
Structure title titleReduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment
Keywords keywordsmetal-binding, membrane protein, IMMUNE SYSTEM-OXIDOREDUCTASE complex; IMMUNE SYSTEM/OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.28 Å
Radius of gyration Rg (electron density) rg_electron39.75 Å
Forward intensity I(0) i0187253000.00
Molecular weight molecular_weight117200.0 kDa
Excluded volume excluded_volume148900 ų
Envelope volume envelope_volume184250 ų
Hydration-shell volume shell_volume42276 ų
Envelope diameter envelope_diameter142.9 Å
Shell Rg shell_rg40.58 Å
Envelope Rg envelope_rg40.41 Å
Shape Rg shape_rg39.70 Å
Total Rg total_rg39.98 Å
Total atoms total_atoms8261
Residues n_residues1029
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax135.4 Å
Rg (real space) rg_real40.11 Å
Rg uncertainty (real space) rg_real_error1.60 Å
I(0) (real space) i0_real1.8730e+08
I(0) uncertainty (real space) i0_real_error3.3890e+06
Rg (reciprocal space) rg_reciprocal39.60 Å
I(0) (reciprocal space) i0_reciprocal187200000.0000
Solution quality estimate total_estimate0.5134
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.5 Å
Skewness Skewness skewness0.693
Kurtosis Kurtosis kurtosis-0.172
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27860000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.585; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.535; Smooth: 0.194
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (11)

▼

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3wfeh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3wfel1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3wfel2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id3wfeB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily10 — Cytochrome c oxidase-like, subunit I domain
Domain ID domain_id3wfeC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3wfeH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3wfeH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3wfeL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3wfeL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (2)

▶

9. Files and Curves (10)