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2bpo

Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A.

Method: X-RAY DIFFRACTION Dmax: 137.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADPH-CYTOCHROM P450 REDUCTASE

SACCHAROMYCES CEREVISIAE

UniProt P16603

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 46–690 Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；295 K；1.6 M AMMONIUM SULFATE 100 MM SODIUM CITRATE, PH 5.0 5 MM NICKEL CHLORIDE 1 MM FMN 1 MM FAD 1 MM NADP, T=22 C. Resolution 2.90 Å R-free 0.268
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 46–690 Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；295 K；1.6 M AMMONIUM SULFATE 100 MM SODIUM CITRATE, PH 5.0 5 MM NICKEL CHLORIDE 1 MM FMN 1 MM FAD 1 MM NADP, T=22 C. Resolution 2.90 Å R-free 0.268

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 2BPO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BF4 A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductases. Deposited 2004-12-03 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 46–690（645 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；293 K；1.6 M AMMONIUM SULFATE,100 MM SODIUM CITRATE (PH 5.0),T=20 C
Resolution 3.00 Å R-free 0.261
2BF4 A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductases. Deposited 2004-12-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 46–690（645 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；293 K；1.6 M AMMONIUM SULFATE,100 MM SODIUM CITRATE (PH 5.0),T=20 C
Resolution 3.00 Å R-free 0.261
2BN4 A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductase Deposited 2005-03-18 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 46–690（645 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；293 K；1.6 M AMMONIUM SULFATE 100 MM SODIUM CITRATE (PH 5.0) 1 MM FAD 1 MM NADPH T=20 C
Resolution 2.91 Å R-free 0.300
2BN4 A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductase Deposited 2005-03-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 47–690（644 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；293 K；1.6 M AMMONIUM SULFATE 100 MM SODIUM CITRATE (PH 5.0) 1 MM FAD 1 MM NADPH T=20 C
Resolution 2.91 Å R-free 0.300
3FJO Structure of chimeric YH CPR Deposited 2008-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–211（168 aa） Fragment：yeast FMN domain, UNP residues 44-211, human FAD domain CPR, UNP residues 232-677
Not recorded FMN FLAVIN MONONUCLEOTIDE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEGII from Nextal condition G11, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.290

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCPR_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 38–682； UniProt 46–690 Author chain B； PDBConstruct 38–682； UniProt 46–690

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 2bpo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bpo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bpo
Deposition date deposition_date2005-04-21
Structure title titleCrystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A.
Keywords keywordsREDUCTASE, NADPH-CYTOCHROME P450 REDUCTASE, CPR, DIFLAVIN REDUCTASE, FAD, FMN-BINDING, NADP, ELECTRON TRANSFER; REDUCTASE
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_guinier41.95 Å
Radius of gyration Rg (electron density) rg_electron42.23 Å
Forward intensity I(0) i0327099000.00
Molecular weight molecular_weight146800.0 kDa
Excluded volume excluded_volume183050 ų
Envelope volume envelope_volume237710 ų
Hydration-shell volume shell_volume49982 ų
Envelope diameter envelope_diameter145.1 Å
Shell Rg shell_rg43.43 Å
Envelope Rg envelope_rg42.11 Å
Shape Rg shape_rg42.21 Å
Total Rg total_rg42.34 Å
Total atoms total_atoms10343
Residues n_residues1282
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 dmax137.3 Å
Rg (real space) rg_real42.36 Å
Rg uncertainty (real space) rg_real_error1.31 Å
I(0) (real space) i0_real3.2710e+08
I(0) uncertainty (real space) i0_real_error6.0810e+06
Rg (reciprocal space) rg_reciprocal41.96 Å
I(0) (reciprocal space) i0_reciprocal327000000.0000
Solution quality estimate total_estimate0.5611
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.1 Å
Skewness Skewness skewness0.575
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66380000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.887; Smooth: 0.207
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id2bpoA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain
Domain ID domain_id2bpoA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id2bpoA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id2bpoA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
Domain ID domain_id2bpoB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain
Domain ID domain_id2bpoB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id2bpoB03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id2bpoB04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
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8. Citations (1)

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9. Files and Curves (10)