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2yvf

Crystal structure of ferredoxin reductase BPHA4 (hydroquinone)

Method: X-RAY DIFFRACTION Dmax: 71.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin reductase

Pseudomonas sp.

UniProt Q52437

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–408 Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 FMT FORMIC ACID × 10 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 5.40, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.60 Å R-free 0.214

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 2YVF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D7Y CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4 Deposited 1999-10-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–408（408 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Sodium formate Acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.228
1F3P FERREDOXIN REDUCTASE (BPHA4)-NADH COMPLEX Deposited 2000-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–408（408 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2.0M Sodium formate, 100mM Na acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.291
2YVG crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone) Deposited 2007-04-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–408（408 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 5.40, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.220
2YVJ Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex Deposited 2007-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–408（408 aa）
Chain P 1–408（408 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES, 30%(W/V) PEG4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.262
8PXK Structure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 5.76 A Deposited 2023-07-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–408（408 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Sodium formate Acetate buffer, pH 4.6
Resolution 3.77 Å R-free 0.191
8PXL Structure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 1.37 A Deposited 2023-07-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–408（408 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 FMT FORMIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Sodium formate Acetate buffer, pH 4.6
Resolution 1.60 Å R-free 0.204

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q52437_PSES1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–408； UniProt 1–408

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 2yvf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2yvf
Deposition date deposition_date2007-04-12
Structure title titleCrystal structure of ferredoxin reductase BPHA4 (hydroquinone)
Keywords keywordsFLAVOPROTEIN, 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_guinier22.61 Å
Radius of gyration Rg (electron density) rg_electron21.80 Å
Forward intensity I(0) i034088800.00
Molecular weight molecular_weight43736.0 kDa
Excluded volume excluded_volume54285 ų
Envelope volume envelope_volume63392 ų
Hydration-shell volume shell_volume24104 ų
Envelope diameter envelope_diameter71.1 Å
Shell Rg shell_rg28.75 Å
Envelope Rg envelope_rg22.06 Å
Shape Rg shape_rg21.80 Å
Total Rg total_rg22.64 Å
Total atoms total_atoms3075
Residues n_residues401
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 dmax71.2 Å
Rg (real space) rg_real22.52 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real3.4090e+07
I(0) uncertainty (real space) i0_real_error4.3820e+05
Rg (reciprocal space) rg_reciprocal22.54 Å
I(0) (reciprocal space) i0_reciprocal34090000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9 Å
Skewness Skewness skewness0.211
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10140000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.967
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2yvfa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd2yvfa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains
Domain ID domain_idd2yvfa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamilyd.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family Family familyd.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Domain ID domain_idd2yvfa4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id2yvfA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2yvfA02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2yvfA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
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8. Citations (1)

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9. Files and Curves (10)