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)

Method: X-RAY DIFFRACTION D_max: 39.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rubredoxin

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

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 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

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 5OME	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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	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 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	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 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 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 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 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 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 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 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 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 ligand/ion 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 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 ligand/ion 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 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 ligand/ion 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 hanging drop；3.8 M sodium/potassium phosphate, hanging drop	Resolution 1.10 Å R-free 0.165
3KYX Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K Deposited 2009-12-07	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	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
3KYY Joint Xray/neutron crystal structure determination of H-labeled perdeuterated rubredoxin at 295K Deposited 2009-12-07	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	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 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	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 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	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 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	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 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	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 ligand/ion 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 ligand/ion 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 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	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 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 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
9BKL Cobalt substituted rubredoxin from Pyrococcus furiosus solved by Co/S-SAD Deposited 2024-04-29	Different ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ome
Deposition date deposition_date	2017-07-31
Structure title title	The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)
Keywords keywords	Perdeuterated rubredoxin, pyrococcus furiosus, atomic resolution, cryofrozen, reduced, iron, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	12.49 Å
Radius of gyration Rg (electron density) rg_electron	10.09 Å
Forward intensity I(0) i0	476713.00
Molecular weight molecular_weight	7061.0 kDa
Excluded volume excluded_volume	9749 Å³
Envelope volume envelope_volume	9144 Å³
Hydration-shell volume shell_volume	7711 Å³
Envelope diameter envelope_diameter	36.5 Å
Shell Rg shell_rg	15.67 Å
Envelope Rg envelope_rg	10.74 Å
Shape Rg shape_rg	10.01 Å
Total Rg total_rg	12.57 Å
Total atoms total_atoms	817
Residues n_residues	54
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	39.9 Å
Rg (real space) rg_real	12.42 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	4.7670e+05
I(0) uncertainty (real space) i0_real_error	4.9870e+03
Rg (reciprocal space) rg_reciprocal	12.42 Å
I(0) (reciprocal space) i0_reciprocal	476700.0000
Solution quality estimate total_estimate	0.7769
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.043
Kurtosis Kurtosis kurtosis	-0.200
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	67480.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.705; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Rubredoxin
Molecular weight formula_weight	6031.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1138

MAKWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAPKSEFEKLED

来源 Source

来源生物 organism	Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
NCBI Class编号 ncbi_taxonomy_id	186497
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5omea_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.1 — Rubredoxin

CATH v4.4 (1 domains)

Domain ID domain_id	5omeA00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	33.993 Å
Unit-cell length b length_b	34.803 Å
Unit-cell length c length_c	43.233 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	0.747 Å
Low-resolution limit resolution_low	18.363 Å
R factor r_factor	0.1115
R_work r_work	0.1110
R_free r_free	0.1214

fit	/app/data/saxs_computation/om/5ome/5ome.fit
pddf	/app/data/pr_computation/om/5ome/5ome.pr.out
profile	/app/data/saxs_computation/om/5ome/5ome.dat