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5y5m

SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)

Method: X-RAY DIFFRACTION Dmax: 101.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADP nitrous oxide-forming nitric oxide reductase

Fusarium oxysporum

UniProt P23295

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 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
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 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

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 5Y5M 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
7DVO Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL Deposited 2021-01-14 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 × 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
7DVO Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL Deposited 2021-01-14 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 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

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

SAXS profile for 5y5m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5y5m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5y5m
Deposition date deposition_date2017-08-09
Structure title titleSFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)
Keywords keywordsmetal-binding, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.14 Å
Radius of gyration Rg (electron density) rg_electron31.44 Å
Forward intensity I(0) i0121653000.00
Molecular weight molecular_weight89272.0 kDa
Excluded volume excluded_volume112470 ų
Envelope volume envelope_volume141610 ų
Hydration-shell volume shell_volume37905 ų
Envelope diameter envelope_diameter101.8 Å
Shell Rg shell_rg38.05 Å
Envelope Rg envelope_rg31.11 Å
Shape Rg shape_rg31.41 Å
Total Rg total_rg32.09 Å
Total atoms total_atoms6284
Residues n_residues798
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax101.2 Å
Rg (real space) rg_real32.17 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real1.2170e+08
I(0) uncertainty (real space) i0_real_error1.8740e+06
Rg (reciprocal space) rg_reciprocal32.16 Å
I(0) (reciprocal space) i0_reciprocal121700000.0000
Solution quality estimate total_estimate0.7145
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.0 Å
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.568
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28160000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.988; Smooth: 0.770
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5y5ma_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450
Domain ID domain_idd5y5mb_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450

CATH v4.4 (2 domains)

Domain ID domain_id5y5mA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5y5mB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
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8. Citations (1)

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9. Files and Curves (10)