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3o0r

Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment

Method: X-RAY DIFFRACTION
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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 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

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 3O0R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 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 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
3WFE Reduced and cyanide-bound 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 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
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 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

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 3O0R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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 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 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
3WFE Reduced and cyanide-bound 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 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
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

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3o0r
Deposition date deposition_date2010-07-20
Structure title titleCrystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment
Keywords keywordsoxidoreductase, electron transport, heme, iron, membrane, cytoplasmic membrane, IMMUNE SYSTEM-OXIDOREDUCTASE complex; IMMUNE SYSTEM/OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3o0rh_
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_idd3o0rl1
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_idd3o0rl2
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_id3o0rB00
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_id3o0rC00
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_id3o0rH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3o0rH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3o0rL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3o0rL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (0)