SAXSdb — 2bf4

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

NADPH-CYTOCHROME P450 REDUCTASE

SACCHAROMYCES CEREVISIAE

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	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 46–690	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

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 2BF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 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
2BPO Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A. Deposited 2005-04-21	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）	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
2BPO Crystal structure of the yeast CPR triple mutant: D74G, Y75F, K78A. Deposited 2005-04-21	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）	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
3FJO Structure of chimeric YH CPR Deposited 2008-12-15	Different construct 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2bf4
Deposition date deposition_date	2004-12-03
Structure title title	A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductases.
Keywords keywords	REDUCTASE, NADPH-CYTOCHROME P450 REDUCTASE, CPR, DIFLAVIN REDUCTASE, FAD, FMN, NADP, ELECTRON TRANSFER; REDUCTASE
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	41.93 Å
Radius of gyration Rg (electron density) rg_electron	42.22 Å
Forward intensity I(0) i0	337863000.00
Molecular weight molecular_weight	148690.0 kDa
Excluded volume excluded_volume	185180 Å³
Envelope volume envelope_volume	236880 Å³
Hydration-shell volume shell_volume	49835 Å³
Envelope diameter envelope_diameter	145.4 Å
Shell Rg shell_rg	43.30 Å
Envelope Rg envelope_rg	42.18 Å
Shape Rg shape_rg	42.21 Å
Total Rg total_rg	42.33 Å
Total atoms total_atoms	10473
Residues n_residues	1290
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	147.1 Å
Rg (real space) rg_real	42.34 Å
Rg uncertainty (real space) rg_real_error	1.92 Å
I(0) (real space) i0_real	3.3790e+08
I(0) uncertainty (real space) i0_real_error	6.8960e+06
Rg (reciprocal space) rg_reciprocal	41.93 Å
I(0) (reciprocal space) i0_reciprocal	337700000.0000
Solution quality estimate total_estimate	0.7730
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.578
Kurtosis Kurtosis kurtosis	-0.382
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	75760000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.566; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.801; Smooth: 0.567

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	NADPH-CYTOCHROME P450 REDUCTASE
Molecular weight formula_weight	75843.0 kDa
EC 编号 ec_number	1.6.2.4
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	10624

MGSSHHHHHHSSGLVPRGSHMLDIMSDDGDITAVSSGNRDIAQVVTENNKNYLVLYASQTGTAEDYAKKFSKELVAKFNLNVMCADVENYDFESLNDVPVIVSIFISTYGEGDFPDGAVNFEDFICNAEAGALSNLRYNMFGLGNSTYEFFNGAAKKAEKHLSAAGAIRLGKLGEADDGAGTTDEDYMAWKDSILEVLKDELHLDEQEAKFTSQFQYTVLNEITDSMSLGEPSAHYLPSHQLNRNADGIQLGPFDLSQPYIAPIVKSRELFSSNDRNCIHSEFDLSGSNIKYSTGDHLAVWPSNPLEKVEQFLSIFNLDPETIFDLKPLDPTVKVPFPTPTTIGAAIKHYLEITGPVSRQLFSSLIQFAPNADVKEKLTLLSKDKDQFAVEITSKYFNIADALKYLSDGAKWDTVPMQFLVESVPQMTPRYYSISSSSLSEKQTVHVTSIVENFPNPELPDAPPVVGVTTNLLRNIQLAQNNVNIAETNLPVHYDLNGPRKLFANYKLPVHVRRSNFRLPSNPSTPVIMIGPGTGVAPFRGFIRERVAFLESQKKGGNNVSLGKHILFYGSRNTDDFLYQDEWPEYAKKLDGSFEMVVAHSRLPNTKKVYVQDKLKDYEDQVFEMINNGAFIYVCGDAKGMAKGVSTALVGILSRGKSITTDEATELIKMLKTSGRYQEDVW

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	151

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2bf4A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

Domain ID domain_id	2bf4A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

Domain ID domain_id	2bf4A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2bf4A04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	2bf4B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

Domain ID domain_id	2bf4B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

Domain ID domain_id	2bf4B03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	2bf4B04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

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8. Citations (1)

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Unit-cell length a length_a	77.751 Å
Unit-cell length b length_b	87.094 Å
Unit-cell length c length_c	259.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	43.550 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2610

fit	/app/data/saxs_computation/bf/2bf4/2bf4.fit
pddf	/app/data/pr_computation/bf/2bf4/2bf4.pr.out
profile	/app/data/saxs_computation/bf/2bf4/2bf4.dat

A second FMN-binding site in yeast NADPH-cytochrome P450 reductase suggests a novel mechanism of electron transfer by diflavin reductases.

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

NADPH-CYTOCHROME P450 REDUCTASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction