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3kyx

Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K

Dmax: 36.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rubredoxin

Pyrococcus furiosus

UniProt P24297

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 1–54 Not recorded FE FE (III) ION × 1 Experimental method not declared X-ray crystallization conditions：hanging drop；3.8 M sodium/potassium phosphate, hanging drop Resolution 1.68 Å R-free 0.197

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 3KYX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BQ8 Rubredoxin (Methionine Mutant) from Pyrococcus Furiosus Deposited 1998-08-22 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；VAPOR DIFFUSION AGAINST 3.6M NA,K PHOSPHATE, pH 8.5, vapor diffusion
Resolution 1.10 Å R-free 0.149
1BQ9 Rubredoxin (Formyl Methionine Mutant) from Pyrococcus Furiosus Deposited 1998-08-22 Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Mutation：FMET INSERTED IN N-TERMINAL POSITION Non-standard monomer：Yes (specific site not provided by mmCIF) FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；VAPOR DIFFUSION AGAINST 3.6M NA,K PHOSPHATE, pH 8.5, vapor diffusion
Resolution 1.20 Å R-free 0.166
1BRF Rubredoxin (Wild Type) from Pyrococcus Furiosus Deposited 1998-08-24 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；VAPOR DIFFUSION AGAINST 3.6M NA,K PHOSPHATE, pH 8.5, vapor diffusion
Resolution 0.95 Å R-free 0.162
1CAA X-RAY CRYSTAL STRUCTURES OF THE OXIDIZED AND REDUCED FORMS OF THE RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS Deposited 1992-05-18 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1CAD X-RAY CRYSTAL STRUCTURES OF THE OXIDIZED AND REDUCED FORMS OF THE RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS Deposited 1992-05-18 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1IU5 X-ray Crystal Structure of the rubredoxin mutant from Pyrococcus Furiosus Deposited 2002-02-27 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Mutation：W3Y, I23V, L32I FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；Na/K phosphate, VAPOR DIFFUSION
Resolution 1.50 Å R-free 0.203
1IU6 Neutron Crystal Structure of the rubredoxin mutant from Pyrococcus Furiosus Deposited 2002-02-27 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Mutation：W3Y, I23V, L32I FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；Na/K phosphate, VAPOR DIFFUSION
Resolution 1.60 Å R-free 0.228
1QCV RUBREDOXIN VARIANT (PFRD-XC4) FOLDS WITHOUT IRON Deposited 1999-05-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Mutation：C5L C8T C38A C41T No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 225mM；Pressure 1
NMR sample composition 1.5MM PFRD-XC4 ACETATE-D3 PH 6.3; 200MM NACL; 90/10 H2O/D2O
Resolution not provided
1RWD Backbone NMR Structure of a Mutant P. Furiosus Rubredoxin Using Residual Dipolar Couplings Deposited 2003-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Mutation：W3Y, I23V, L32I No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient
NMR sample composition 4.5 mM Rubredoxin U-15N; 50 mM Na Phosphate; 100 mM NaCl; pH 6.3 | 90% H2O/10% D2O
NMR sample composition 2.5 mM Rubredoxin U-15N; 50 mM Na Phosphate ; 50 mM NaCl; pH 6.3; 7% Bicelle (3:1 DMPC:DHPC with 4% CTAB relative to DMPC) | Bicelles in 90% H2O, 10% D2O
NMR sample composition 4.5 mM Rubredoxin U-15N; 50 mM Na Phosphate; 100 mM NaCl; pH 6.3; PF1 phage sample | Phage in 90% H2O, 10% D2O
Resolution not provided
1VCX Neutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution Deposited 2004-03-17 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Not recorded FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions Macroseeding；pH 8；298 K；sodium dihydrogen phosphate, dipotassium hydrogen phosphate, pH 8.0, Macroseeding, temperature 298K
Resolution 1.50 Å R-free 0.217
1ZRP SOLUTION-STATE STRUCTURE BY NMR OF ZINC-SUBSTITUTED RUBREDOXIN FROM THE MARINE HYPERTHERMOPHILIC ARCHAEBACTERIUM PYROCOCCUS FURIOSUS Deposited 1992-07-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–53（53 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
2PVX NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-10 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–54（54 aa）
Mutation：A2K,K7T,I8V,I41L,A44V,P45G,S47D,E48Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；62% Ammonium Sulphate 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.04 Å R-free 0.180
3KYU X-ray crystal structure determination of fully perdeuterated rubredoxin at 100K Deposited 2009-12-07 Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；3.8 M sodium/potassium phosphate, hanging drop
Resolution 1.10 Å R-free 0.125
3KYV Denovo X-ray crystal structure determination of H-labeled perdeuterated rubredoxin at 100K Deposited 2009-12-07 Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；3.8 M sodium/potassium phosphate, hanging drop
Resolution 1.10 Å R-free 0.147
3KYW Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K Deposited 2009-12-07 Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；3.8 M sodium/potassium phosphate, hanging drop
Resolution 1.10 Å R-free 0.165
3KYY Joint Xray/neutron crystal structure determination of H-labeled perdeuterated rubredoxin at 295K Deposited 2009-12-07 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 Experimental method not declared
X-ray crystallization conditions 3.8 M sodium/potassium phosphate, hanging drop
Resolution 1.10 Å
3RYG 128 hours neutron structure of perdeuterated rubredoxin Deposited 2011-05-11 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 mg/ml rubredoxin in 1.9 M sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.200
3RZ6 Neutron structure of perdeuterated rubredoxin using 40 hours 1st pass data Deposited 2011-05-11 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 mg/ml rubredoxin in 1.9 M sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.238
3RZT Neutron structure of perdeuterated rubredoxin using rapid (14 hours) data Deposited 2011-05-12 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 mg/ml rubredoxin in 1.9 M sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.249
3SS2 Neutron structure of perdeuterated rubredoxin using 48 hours 3rd pass data Deposited 2011-07-07 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 mg/ml rubredoxin in 1.9m sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.242
4AR3 Near-atomic resolution neutron crystallography on the oxidised form perdeuterated Pyrococcus furiosus rubredoxin. Deposited 2012-04-20 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 D8U deuterium(1+) × 4 D3O trideuteriooxidanium × 4 NEUTRON DIFFRACTION
X-ray crystallization conditions pH 6.5；PH 6.5
Resolution 1.05 Å R-free 0.237
4AR4 Neutron crystallographic structure of the reduced form perdeuterated Pyrococcus furiosus rubredoxin to 1.38 Angstrom resolution. Deposited 2012-04-20 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 D8U deuterium(1+) × 2 D3O trideuteriooxidanium × 4 NEUTRON DIFFRACTION
X-ray crystallization conditions pH 6.2；pH 6.2
Resolution 1.38 Å R-free 0.226
4AR5 X-ray crystallographic structure of the oxidised form perdeuterated Pyrococcus furiosus rubredoxin in D2O at 295K (in quartz capillary) to 1.00 Angstrom resolution. Deposited 2012-04-20 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.00 Å R-free 0.119
4AR6 X-ray crystallographic structure of the reduced form perdeuterated Pyrococcus furiosus rubredoxin at 295 K (in quartz capillary) to 0.92 Angstroms resolution. Deposited 2012-04-20 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；pH 6.2
Resolution 0.92 Å R-free 0.136
4K9F Neutron structure of Perdeuterated Rubredoxin refined against 1.75 resolution data collected on the new IMAGINE instrument at HFIR, ORNL Deposited 2013-04-19 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NEUTRON DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 mg/ml rubredoxin in 1.9 M SODIUM/POTASSIUM PHOSPHATE sitting drop equilibrated against 3.8 M SODIUM/POTASSIUM PHOSPHATE reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.241
5AI2 Anomalous Neutron phased crystal structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.75A resolution at 295K Deposited 2015-02-11 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded CD CADMIUM ION × 1 D8U deuterium(1+) × 3 NEUTRON DIFFRACTION
X-ray crystallization conditions pH 6.5；PH 6.5
Resolution 1.75 Å R-free 0.286
5AI3 X-ray structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.02A resolution at 295K in a quartz capillary Deposited 2015-02-11 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；3.8 M NAH2PO4, 3.8M K2HPO4 IN MORE THAN 99.7 PERCENT PURE D2O, pH 6.5
Resolution 1.02 Å R-free 0.126
5NW3 The cryofrozen atomic resolution X-ray crystal structure of perdeuterated Pyrococcus furiosus Rubredoxin (100K, 0.59A resolution) Deposited 2017-05-04 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NA SODIUM ION × 1 K POTASSIUM ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；seeded 3.4M equimolar Na/K phosphate buffer
Resolution 0.59 Å R-free 0.146
5OME The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution) Deposited 2017-07-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 NA SODIUM ION × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；SEEDED 3.4M EQUIMOLAR NA/K PHOSPHATE BUFFER
Resolution 0.75 Å R-free 0.121
9BKL Cobalt substituted rubredoxin from Pyrococcus furiosus solved by Co/S-SAD Deposited 2024-04-29 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.8M NaH2PO4, 3.8M K2HPO4 (1:1, v/v)
Resolution 1.70 Å R-free 0.183
9BKP Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeCl3 solved by Fe/S-SAD Deposited 2024-04-29 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M Tris pH 8.4, 2.2M ammonium sulfate, 30% MPD
Resolution 1.80 Å R-free 0.185
9BKT Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeSO4 solved by Fe/S-SAD Deposited 2024-04-29 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded FE2 FE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M tris pH 8.4 2.2 M ammonium sulfate 30% MPD
Resolution 1.80 Å R-free 0.166
9XZU Rubredoxin from Pyrococcus Furiosus at 100K, Alanine-2 N terminus Deposited 2025-08-27 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.82 Å R-free 0.148
9Y00 Zinc Rubredoxin from Pyrococcus Furiosus at 140K, A2 Nterminus Deposited 2025-08-28 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.83 Å R-free 0.140
9Y0Y Rubredoxin from Pyrococcus Furiosus at 180K, Alanine-2 N terminus Deposited 2025-08-29 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.85 Å R-free 0.150
9Y0Z Rubredoxin from Pyrococcus Furiosus at 200K, Alanine-2 N terminus Deposited 2025-08-29 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.86 Å R-free 0.149
9Y11 Zn Rubredoxin from Pyrococcus Furiosus at 220K, Alanine-2 N terminus Deposited 2025-08-29 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.91 Å R-free 0.147
9Y1U Rubredoxin from Pyrococcus Furiosus at 240K, Alanine-2 N terminus Deposited 2025-08-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.98 Å R-free 0.148
9Y28 Rubredoxin from Pyrococcus Furiosus at 260K, Alanine-2 N terminus Deposited 2025-08-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.01 Å R-free 0.143
9Y29 Rubredoxin from Pyrococcus Furiosus at 280K, Alanine-2 N terminus Deposited 2025-08-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.08 Å R-free 0.144
9Y2E Rubredoxin from Pyrococcus Furiosus at 100K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 0.78 Å R-free 0.140
9Y2G Rubredoxin from Pyrococcus Furiosus at 293K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.14 Å R-free 0.158
9Y2Y Rubredoxin from Pyrococcus Furiosus at 393K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.68 Å R-free 0.243
9Y30 Rubredoxin from Pyrococcus Furiosus at 383K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.53 Å R-free 0.190
9Y32 Rubredoxin from Pyrococcus Furiosus at 373K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.47 Å R-free 0.173
9Y33 Rubredoxin from Pyrococcus Furiosus at 363K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.35 Å R-free 0.154
9Y37 Rubredoxin from Pyrococcus Furiosus at 353K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.84 Å R-free 0.253
9Y38 Rubredoxin from Pyrococcus Furiosus at 313K, formyl-Methionine N-terminus Deposited 2025-09-01 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–54（54 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Resolution 1.41 Å R-free 0.195

48 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RUBR_PYRFU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–54； UniProt 1–54

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 3kyx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3kyx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3kyx
Deposition date deposition_date2009-12-07
Structure title titleJoint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K
Keywords keywordsjoint X-ray neutron refinement, Electron transport, Iron, Metal-binding, Transport; ELECTRON TRANSPORT
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.08 Å
Radius of gyration Rg (electron density) rg_electron9.80 Å
Forward intensity I(0) i0504375.00
Molecular weight molecular_weight7069.0 kDa
Excluded volume excluded_volume9688 ų
Envelope volume envelope_volume9219 ų
Hydration-shell volume shell_volume7835 ų
Envelope diameter envelope_diameter31.5 Å
Shell Rg shell_rg15.70 Å
Envelope Rg envelope_rg10.46 Å
Shape Rg shape_rg9.78 Å
Total Rg total_rg12.09 Å
Total atoms total_atoms832
Residues n_residues52
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 dmax36.2 Å
Rg (real space) rg_real11.98 Å
Rg uncertainty (real space) rg_real_error0.16 Å
I(0) (real space) i0_real5.0440e+05
I(0) uncertainty (real space) i0_real_error5.2800e+03
Rg (reciprocal space) rg_reciprocal11.99 Å
I(0) (reciprocal space) i0_reciprocal504400.0000
Solution quality estimate total_estimate0.8887
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness-0.004
Kurtosis Kurtosis kurtosis-0.300
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha103000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.951
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3kyxa_
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.5 — Rubredoxin-like
Family Family familyg.41.5.1 — Rubredoxin

CATH v4.4 (1 domains)

Domain ID domain_id3kyxA00
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)