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1kek

Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase

Method: X-RAY DIFFRACTION Dmax: 124.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate-Ferredoxin Oxidoreductase

OrganismNot specified

UniProt P94692

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 2–1232 Chain B； UniProt 2–1232 Not recorded MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 6 HTL 2-ACETYL-THIAMINE DIPHOSPHATE × 2 CO2 CARBON DIOXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；PEG 6000 10-15%, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.90 Å R-free 0.227

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 1KEK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B0P CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS Deposited 1998-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 6 TPP THIAMINE DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；CRYSTALLIZATION CONDITIONS: PEG6000 11% MGCL2 100MM CACODYLATE 100MM PH 6.0
Resolution 2.31 Å R-free 0.271
2C3M Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus Deposited 2005-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 TPP THIAMINE DIPHOSPHATE × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；10% PEG6000, 100MM MGCL2, 100MM TRIS-HCL PH9, pH 9.00
Resolution 1.84 Å R-free 0.222
2C3O CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus Deposited 2005-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 TPP THIAMINE DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 PYR PYRUVIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；10% PEG6000, 100MM MGCL2, 100 MM NA CACODYLATE PH 6
Resolution 2.70 Å R-free 0.268
2C3P CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus Deposited 2005-10-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 1TP 1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE PH 6
Resolution 2.33 Å R-free 0.223
2C3U Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus, Oxygen inhibited form Deposited 2005-10-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 2TP 2-(3-{[4-(HYDROXYAMINO)-2-METHYLPYRIMIDIN-5-YL]METHYL}-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL)ETHYL TRIHYDROGEN DIPHOSPHATE × 2 PYR PYRUVIC ACID × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；10% PEG6000, 100MM MGCL2, 100MM TRIS-HCL PH 9
Resolution 2.32 Å R-free 0.238
2C3Y CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus Deposited 2005-10-13 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 HTL 2-ACETYL-THIAMINE DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 CO2 CARBON DIOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；10% PEG6000, 100MM MGCL2, 100MM TRIS-HCL PH 9
Resolution 1.93 Å R-free 0.228
2C42 Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus Deposited 2005-10-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 TPP THIAMINE DIPHOSPHATE × 2 PYR PYRUVIC ACID × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE, 5% DTT, pH 6.00
Resolution 1.78 Å R-free 0.219
2PDA CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE. Deposited 1998-11-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa）
Chain B 2–1232（1231 aa）
Not recorded MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 6 TPP THIAMINE DIPHOSPHATE × 2 PYR PYRUVIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；PEG6000 11% MGCL2 100MM CACODYLATE 100MM PH 6.2 PYRUVATE 100MM
Resolution 3.00 Å R-free 0.297
2UZA CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS Deposited 2007-04-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–1232（1231 aa） Fragment：RESIDUES 2-1232
Chain B 2–1232（1231 aa） Fragment：RESIDUES 2-1232
Not recorded SF4 IRON/SULFUR CLUSTER × 6 HTL 2-ACETYL-THIAMINE DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 CO2 CARBON DIOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE PH 6
Resolution 2.42 Å R-free 0.226
7PLM CryoEM reconstruction of pyruvate ferredoxin oxidoreductase (PFOR) in anaerobic conditions Deposited 2021-08-31 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–1232（1232 aa）
Chain B 1–1232（1232 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 6 TPP THIAMINE DIPHOSPHATE × 2 CA CALCIUM ION × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.4
cryo-EM vitrification conditions Cryogen PROPANE
Resolution 2.90 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P94692_DESAF
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1231； UniProt 2–1232 Author chain B； PDBConstruct 1–1231； UniProt 2–1232

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 1kek

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1kek
Deposition date deposition_date2001-11-16
Structure title titleCrystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase
Keywords keywordshomodimer, 7 domains, 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_guinier39.04 Å
Radius of gyration Rg (electron density) rg_electron38.62 Å
Forward intensity I(0) i01107070000.00
Molecular weight molecular_weight270350.0 kDa
Excluded volume excluded_volume336480 ų
Envelope volume envelope_volume403390 ų
Hydration-shell volume shell_volume81027 ų
Envelope diameter envelope_diameter134.6 Å
Shell Rg shell_rg47.88 Å
Envelope Rg envelope_rg39.23 Å
Shape Rg shape_rg38.60 Å
Total Rg total_rg39.11 Å
Total atoms total_atoms18882
Residues n_residues2462
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 dmax124.1 Å
Rg (real space) rg_real38.87 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real1.1070e+09
I(0) uncertainty (real space) i0_real_error1.8400e+07
Rg (reciprocal space) rg_reciprocal38.98 Å
I(0) (reciprocal space) i0_reciprocal1107000000.0000
Solution quality estimate total_estimate0.8756
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.5 Å
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.243
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha303100000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.775
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd1keka1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.8 — PFOR Pyr module
Domain ID domain_idd1keka2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.12 — PFOR PP module
Domain ID domain_idd1keka3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
Domain ID domain_idd1keka4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Superfamily Superfamily superfamilyc.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Family Family familyc.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_idd1keka5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.1 — 4Fe-4S ferredoxins
Family Family familyd.58.1.5 — Ferredoxin domains from multidomain proteins
Domain ID domain_idd1kekb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.8 — PFOR Pyr module
Domain ID domain_idd1kekb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.12 — PFOR PP module
Domain ID domain_idd1kekb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
Domain ID domain_idd1kekb4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Superfamily Superfamily superfamilyc.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Family Family familyc.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_idd1kekb5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.1 — 4Fe-4S ferredoxins
Family Family familyd.58.1.5 — Ferredoxin domains from multidomain proteins

CATH v4.4 (14 domains)

Domain ID domain_id1kekA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1kekA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id1kekA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology920 — Pyruvate-ferredoxin Oxidoreductase; domain 3
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_id1kekA04
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology780 — Pyruvate-ferredoxin Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Pyruvate-flavodoxin oxidoreductase, EKR domain
Domain ID domain_id1kekA05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1kekA06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1kekA07
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology790 — Pyruvate-ferredoxin Oxidoreductase; domain 7
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin Oxidoreductase; domain 7
Domain ID domain_id1kekB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1kekB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id1kekB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology920 — Pyruvate-ferredoxin Oxidoreductase; domain 3
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_id1kekB04
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology780 — Pyruvate-ferredoxin Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Pyruvate-flavodoxin oxidoreductase, EKR domain
Domain ID domain_id1kekB05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1kekB06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1kekB07
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology790 — Pyruvate-ferredoxin Oxidoreductase; domain 7
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin Oxidoreductase; domain 7
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8. Citations (1)

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9. Files and Curves (10)