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8pxl

Structure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 1.37 A

Method: X-RAY DIFFRACTION Dmax: 70.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferredoxin reductase

Pseudomonas sp. KKS102

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–408 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

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 8PXL 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 oligomeric state 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 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
2YVF Crystal structure of ferredoxin reductase BPHA4 (hydroquinone) Deposited 2007-04-12 Different oligomeric state 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 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
2YVG crystal structure of ferredoxin reductase, BPHA4 (blue-semiquinone) Deposited 2007-04-12 Different oligomeric state 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 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 ligand/ion 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

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 8pxl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8pxl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8pxl
Deposition date deposition_date2023-07-23
最后修订 last_revision2023-10-25
Structure title titleStructure of NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4, solved at wavelength 1.37 A
Keywords keywordsBPHA4, 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_guinier23.03 Å
Radius of gyration Rg (electron density) rg_electron22.10 Å
Forward intensity I(0) i033723300.00
Molecular weight molecular_weight43772.0 kDa
Excluded volume excluded_volume54498 ų
Envelope volume envelope_volume64616 ų
Hydration-shell volume shell_volume24352 ų
Envelope diameter envelope_diameter71.3 Å
Shell Rg shell_rg28.99 Å
Envelope Rg envelope_rg22.23 Å
Shape Rg shape_rg22.09 Å
Total Rg total_rg22.95 Å
Total atoms total_atoms3079
Residues n_residues403
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 dmax70.7 Å
Rg (real space) rg_real22.93 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real3.3720e+07
I(0) uncertainty (real space) i0_real_error3.7010e+05
Rg (reciprocal space) rg_reciprocal22.95 Å
I(0) (reciprocal space) i0_reciprocal33720000.0000
Solution quality estimate total_estimate0.9114
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.548
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9540000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.990
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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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8. Citations (1)

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9. Files and Curves (10)