2yvj

Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex

Method: X-RAY DIFFRACTION Dmax: 108.1 Å Quality: GOOD

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–408 Chain P; UniProt 1–408 Not recorded Biphenyl dioxygenase ferredoxin subunit × 1 (Q52440) 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

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.

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 Author chain P; PDBConstruct 1–408; UniProt 1–408

Biphenyl dioxygenase ferredoxin subunit

Pseudomonas sp.

UniProt Q52440

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–109 Not recorded Ferredoxin reductase × 2 (Q52437) 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

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.

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPHA3_PSES1
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–109; UniProt 1–109

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 2yvj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2yvj
Deposition date deposition_date2007-04-12
Structure title titleCrystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex
Keywords keywordselectron transfer, ferredoxin, ferredoxin reductase, OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX; OXIDOREDUCTASE/ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.61
Radius of gyration Rg (electron density) rg_electron32.15
Forward intensity I(0) i0163163000.00
Molecular weight molecular_weight99230.0 kDa
Excluded volume excluded_volume123180 ų
Envelope volume envelope_volume153790 ų
Hydration-shell volume shell_volume39966 ų
Envelope diameter envelope_diameter113.3
Shell Rg shell_rg38.94
Envelope Rg envelope_rg31.85
Shape Rg shape_rg32.15
Total Rg total_rg32.66
Total atoms total_atoms6967
Residues n_residues909
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax108.1
Rg (real space) rg_real32.60
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real1.6320e+08
I(0) uncertainty (real space) i0_real_error2.3460e+06
Rg (reciprocal space) rg_reciprocal32.61
I(0) (reciprocal space) i0_reciprocal163200000.0000
Solution quality estimate total_estimate0.8876
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.7
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha47280000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.879

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd2yvja1
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_idd2yvja2
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_idd2yvja3
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_idd2yvja4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2yvjb_
Class classb — All beta proteins
Fold Fold foldb.33 — ISP domain
Superfamily Superfamily superfamilyb.33.1 — ISP domain
Family Family familyb.33.1.1 — Rieske iron-sulfur protein (ISP)
Domain ID domain_idd2yvjp1
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_idd2yvjp2
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_idd2yvjp3
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_idd2yvjp4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (7 domains)

Domain ID domain_id2yvjA01
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_id2yvjA02
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_id2yvjA03
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
Domain ID domain_id2yvjB00
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id2yvjP01
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_id2yvjP02
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_id2yvjP03
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

8. Citations (1)

9. Files and Curves (10)