7dvo

Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL

Method: X-RAY DIFFRACTION D_max: 99.7 Å Quality: GOOD

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

NADP nitrous oxide-forming nitric oxide reductase

Fusarium oxysporum

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–403	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 8.5；293 K；38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 1.80 Å R-free 0.219
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–403	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：BATCH MODE；pH 8.5；293 K；38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 1.80 Å R-free 0.219

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 7DVO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CL6 CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND ITS SER286 MUTANTS AT CRYOGENIC TEMPERATURE Deposited 1999-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM-MES BUFFER AT PH 7.0 USING PEG 4K	Resolution 1.70 Å R-free 0.251
1CMJ CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND THEIR SER286 MUTANTS AT CRYOGENIC TEMPERATURE Deposited 1999-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：S286T	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM-MES BUFFER AT PH 7.0 USING PEG4K	Resolution 1.70 Å R-free 0.250
1CMN CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND THEIR SER286 MUTANTS AT CRYOGENIC TEMPERATURE Deposited 1999-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：S286V	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；100MM-MES BUFFER AT PH 7.0 USING PEG4K	Resolution 1.70 Å R-free 0.228
1EHE CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S Deposited 2000-02-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；protein was crystallized from 100mM-Mes buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.272
1EHF CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S Deposited 2000-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：S286T	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；protein was crystallized from 100mM-Mes buffer , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.265
1EHG CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S Deposited 2000-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：S286V	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；protein was crystallized from 100mM-Mes buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.223
1F24 CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ALA MUTANTS OF CYTOCHROME P450NOR Deposited 2000-05-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：T243A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350, MES, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.40 Å R-free 0.207
1F25 CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROME P450NOR Deposited 2000-05-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：T243N	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350, MES, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.40 Å R-free 0.204
1F26 CRYSTAL STRUCTURE OF NO COMPLEX OF THR243VAL MUTANTS OF CYTOCHROME P450NOR Deposited 2000-05-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：T243V	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350, MES, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.40 Å R-free 0.207
1GED A positive charge route for the access of nadh to heme formed in the distal heme pocket of cytochrome p450nor Deposited 2000-11-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	BR BROMIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.279
1GEI STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM Deposited 2000-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NBN N-BUTYL ISOCYANIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.258
1GEJ STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM Deposited 2000-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NBN N-BUTYL ISOCYANIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.50 Å R-free 0.241
1JFB X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferric resting state at atomic resolution Deposited 2001-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–404（404 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350, MES, Glycerol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.00 Å R-free 0.139
1JFC X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferrous CO state at atomic resolution Deposited 2001-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–404（404 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CMO CARBON MONOXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350, MES, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.05 Å R-free 0.152
1ROM CRYSTAL STRUCTURE OF NITRIC REDUCTASE FROM DENITRIFYING FUNGUS FUSARIUM OXYSPORUM Deposited 1997-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 100MM-MES BUFFER AT PH5.5 USING PEG4000 AS PRECIPITANT	Resolution 2.00 Å R-free 0.266
1ULW Crystal structure of P450nor Ser73Gly/Ser75Gly mutant Deposited 2003-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Mutation：S73G, S75G	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；PEG8000, 0.2M sodium acetate, sodium cacodylate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 2.00 Å R-free 0.248
1XQD Crystal structure of P450NOR complexed with 3-pyridinealdehyde adenine dinucleotide Deposited 2004-10-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–402（403 aa）	Mutation：S73G/S75G	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 DND NICOTINIC ACID ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；PEG 8000, sodium acetate, sodium cacodylate, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 1.80 Å R-free 0.243
2ROM CRYSTAL STRUCTURE OF NITRIC REDUCTASE FROM DENITRIFYING FUNGUS FUSARIUM OXYSPORUM COMPLEX WITH CARBON MONOXIDE Deposited 1997-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–402（402 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CMO CARBON MONOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 100MM-MES BUFFER AT PH5.5 USING PEG4000 AS PRECIPITANT	Resolution 2.00 Å R-free 0.269
5Y5F Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray Deposited 2017-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa） Fragment：nitric-oxide reductase cytochrome P450	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；17% PEG 10000, 0.1 M BIS-TRIS 0.1 M Ammonium acetate	Resolution 1.50 Å R-free 0.186
5Y5G Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；17% PEG 10000, 0.1 M BIS-TRIS 0.1 M Ammonium acetate	Resolution 1.36 Å R-free 0.166
5Y5H SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA Deposited 2017-08-09	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa） Fragment：nitric-oxide reductase cytochrome P450	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 1.50 Å R-free 0.196
5Y5I Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data Deposited 2017-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa） Fragment：nitric-oxide reductase cytochrome P450	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.196
5Y5I Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data Deposited 2017-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–403（403 aa） Fragment：nitric-oxide reductase cytochrome P450	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.196
5Y5J Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state) Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.00 Å R-free 0.197
5Y5J Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state) Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.00 Å R-free 0.197
5Y5K Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.194
5Y5K Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.194
5Y5L Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state) Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.193
5Y5L Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state) Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.193
5Y5M SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state) Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.218
5Y5M SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state) Deposited 2017-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–403（403 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8.5；293 K；34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate	Resolution 2.10 Å R-free 0.218

26 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NOR_FUSOX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–403； UniProt 1–403 Author chain B； PDBConstruct 1–403； UniProt 1–403

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7dvo
Deposition date deposition_date	2021-01-14
Structure title title	Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL
Keywords keywords	heme enzyme, oxidoreductase, METAL BINDING PROTEIN; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.95 Å
Radius of gyration Rg (electron density) rg_electron	31.26 Å
Forward intensity I(0) i0	123259000.00
Molecular weight molecular_weight	89700.0 kDa
Excluded volume excluded_volume	112970 Å³
Envelope volume envelope_volume	140710 Å³
Hydration-shell volume shell_volume	37833 Å³
Envelope diameter envelope_diameter	101.9 Å
Shell Rg shell_rg	37.84 Å
Envelope Rg envelope_rg	30.99 Å
Shape Rg shape_rg	31.24 Å
Total Rg total_rg	31.91 Å
Total atoms total_atoms	6312
Residues n_residues	798
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	99.7 Å
Rg (real space) rg_real	31.99 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.2330e+08
I(0) uncertainty (real space) i0_real_error	1.9900e+06
Rg (reciprocal space) rg_reciprocal	31.97 Å
I(0) (reciprocal space) i0_reciprocal	123300000.0000
Solution quality estimate total_estimate	0.8844
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.9 Å
Skewness Skewness skewness	0.331
Kurtosis Kurtosis kurtosis	-0.562
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29820000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.674

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NADP nitrous oxide-forming nitric oxide reductase
Molecular weight formula_weight	44420.7 kDa
EC 编号 ec_number	1.7.1.14
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6969

MASGAPSFPFSRASGPEPPAEFAKLRATNPVSQVKLFDGSLAWLVTKHKDVCFVATSEKLSKVRTRQGFPELSASGKQAAKAKPTFVDMDPPEHMHQRSMVEPTFTPEAVKNLQPYIQRTVDDLLEQMKQKGCANGPVDLVKEFALPVPSYIIYTLLGVPFNDLEYLTQQNAIRTNGSSTAREASAANQELLDYLAILVEQRLVEPKDDIISKLCTEQVKPGNIDKSDAVQIAFLLLVAGNATMVNMIALGVATLAQHPDQLAQLKANPSLAPQFVEELCRYHTASALAIKRTAKEDVMIGDKLVRANEGIIASNQSANRDEEVFENPDEFNMNRKWPPQDPLGFGFGDHRCIAEHLAKAELTTVFSTLYQKFPDLKVAVPLGKINYTPLNRDVGIVDLPVIF

来源 Source

来源生物 organism	Fusarium oxysporum
通用名 common_name	Fusarium vascular wilt
NCBI Class编号 ncbi_taxonomy_id	5507
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NITRIC OXIDE
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	592

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7dvoa_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.1 — Cytochrome P450

Domain ID domain_id	d7dvob_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.1 — Cytochrome P450

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8. Citations (1)

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Unit-cell length a length_a	54.270 Å
Unit-cell length b length_b	101.610 Å
Unit-cell length c length_c	73.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.780 Å
R factor r_factor	0.1750
R_work r_work	0.1727
R_free r_free	0.2191

fit	/app/data/saxs_computation/dv/7dvo/7dvo.fit
pddf	/app/data/pr_computation/dv/7dvo/7dvo.pr.out
profile	/app/data/saxs_computation/dv/7dvo/7dvo.dat