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1b25

FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS

Method: X-RAY DIFFRACTION Dmax: 139.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE)

OrganismNot specified

UniProt O93738

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain not uniquely mapped； UniProt —–— Chain A； UniProt 1–619 Fragment：DOMAIN 1: 1-208, DOMAIN 2: 209-406, DOMAIN 3: 407-619 SF4 IRON/SULFUR CLUSTER × 4 PTT Oxo-tungstopterin cofactor × 4 MG MAGNESIUM ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6 Resolution 1.85 Å R-free 0.220

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 1B25 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B4N FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, COMPLEXED WITH GLUTARATE Deposited 1998-12-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–619（619 aa） Fragment：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619
Chain B 1–619（619 aa） Fragment：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619
Chain C 1–619（619 aa） Fragment：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619
Chain D 1–619（619 aa） Fragment：DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619
Not recorded CA CALCIUM ION × 4 SF4 IRON/SULFUR CLUSTER × 4 GUA GLUTARIC ACID × 4 PTE TUNGSTOPTERIN COFACTOR × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.40 Å R-free 0.244

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O93738_PYRFU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–619； UniProt 1–619

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 1b25

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b25
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b25
Deposition date deposition_date1998-12-04
Structure title titleFORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS
Keywords keywordsMOCO, TUNGSTOENZYME, TUNGSTEN CONTAINING PROTEIN, HYPERTHERMOPHILE, 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_guinier46.11 Å
Radius of gyration Rg (electron density) rg_electron45.97 Å
Forward intensity I(0) i01096230000.00
Molecular weight molecular_weight277190.0 kDa
Excluded volume excluded_volume346640 ų
Envelope volume envelope_volume428230 ų
Hydration-shell volume shell_volume73587 ų
Envelope diameter envelope_diameter145.0 Å
Shell Rg shell_rg54.89 Å
Envelope Rg envelope_rg44.95 Å
Shape Rg shape_rg46.07 Å
Total Rg total_rg45.89 Å
Total atoms total_atoms19384
Residues n_residues2444
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 dmax139.4 Å
Rg (real space) rg_real45.89 Å
Rg uncertainty (real space) rg_real_error1.04 Å
I(0) (real space) i0_real1.0960e+09
I(0) uncertainty (real space) i0_real_error1.9620e+07
Rg (reciprocal space) rg_reciprocal46.11 Å
I(0) (reciprocal space) i0_reciprocal1097000000.0000
Solution quality estimate total_estimate0.8696
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary69.7 Å
Skewness Skewness skewness0.025
Kurtosis Kurtosis kurtosis-0.722
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha384900000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.532
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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) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1b25a1
Class classa — All alpha proteins
Fold Fold folda.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Superfamily Superfamily superfamilya.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Family Family familya.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Domain ID domain_idd1b25a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Superfamily Superfamily superfamilyd.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Family Family familyd.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_idd1b25b1
Class classa — All alpha proteins
Fold Fold folda.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Superfamily Superfamily superfamilya.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Family Family familya.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Domain ID domain_idd1b25b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Superfamily Superfamily superfamilyd.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Family Family familyd.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_idd1b25c1
Class classa — All alpha proteins
Fold Fold folda.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Superfamily Superfamily superfamilya.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Family Family familya.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Domain ID domain_idd1b25c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Superfamily Superfamily superfamilyd.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Family Family familyd.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_idd1b25d1
Class classa — All alpha proteins
Fold Fold folda.110 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Superfamily Superfamily superfamilya.110.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Family Family familya.110.1.1 — Aldehyde ferredoxin oxidoreductase, C-terminal domains
Domain ID domain_idd1b25d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.152 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Superfamily Superfamily superfamilyd.152.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Family Family familyd.152.1.1 — Aldehyde ferredoxin oxidoreductase, N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id1b25A01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_id1b25A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2
Domain ID domain_id1b25A03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3
Domain ID domain_id1b25B01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_id1b25B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2
Domain ID domain_id1b25B03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3
Domain ID domain_id1b25C01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_id1b25C02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2
Domain ID domain_id1b25C03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3
Domain ID domain_id1b25D01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology9 — Aldehyde Ferredoxin Oxidoreductase; A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde ferredoxin oxidoreductase, N-terminal domain
Domain ID domain_id1b25D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology569 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2
Domain ID domain_id1b25D03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology599 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3
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8. Citations (2)

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9. Files and Curves (10)