4rxn

CRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 35.7 Å Quality: GOOD

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

RUBREDOXIN

Clostridium pasteurianum

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	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.20 Å

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 4RXN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B13 CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10A MUTANT Deposited 1998-11-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：G10A	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4.6.	Resolution 1.50 Å R-free 0.191
1B2J CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G43A MUTANT Deposited 1998-11-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：G43A	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4.5., pH 4.6	Resolution 1.60 Å R-free 0.234
1B2O CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10VG43A MUTANT Deposited 1998-11-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：G10V, G43A	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLISED FROM 70% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 5.0.	Resolution 1.90 Å R-free 0.237
1B2O CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10VG43A MUTANT Deposited 1998-11-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa）	Mutation：G10V, G43A	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLISED FROM 70% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 5.0.	Resolution 1.90 Å R-free 0.237
1BE7 CLOSTRIDIUM PASTEURIANUM RUBREDOXIN C42S MUTANT Deposited 1998-05-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–54（54 aa）	Mutation：C42S	FE FE (III) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4., pH 4.0	Resolution 1.65 Å R-free 0.201
1BFY SOLUTION STRUCTURE OF REDUCED CLOSTRIDIUM PASTEURIANUM RUBREDOXIN, NMR, 20 STRUCTURES Deposited 1998-05-23	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	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.1 M；Pressure NORMAL NMR sample composition WATER	Resolution not provided
1C09 RUBREDOXIN V44A CP Deposited 1999-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–54（54 aa） Chain B 1–54（54 aa） Chain C 1–54（54 aa）	Mutation：V44A Mutation：V44A Mutation：V44A	FE FE (III) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；281 K；0.1M Na acetate pH 4.5, 2M ammonium sulfate, temperature 281K	Resolution 1.60 Å
1FHH X-RAY CRYSTAL STRUCTURE OF OXIDIZED RUBREDOXIN Deposited 2000-08-01	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；pH 4.6；277 K；2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å
1FHM X-RAY CRYSTAL STRUCTURE OF REDUCED RUBREDOXIN Deposited 2000-08-02	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；pH 4.6；277 K；2M ammonium sulfate, 0.1M sodium acetate, 0.1 g sodium dithionite, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å
1IRN RUBREDOXIN (ZN-SUBSTITUTED) AT 1.2 ANGSTROMS RESOLUTION Deposited 1995-12-13	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–54（54 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；pH 4.0	Resolution 1.20 Å
1IRO RUBREDOXIN (OXIDIZED, FE(III)) AT 1.1 ANGSTROMS RESOLUTION Deposited 1995-12-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–54（54 aa）	Not recorded	FE FE (III) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；pH 4.0	Resolution 1.10 Å
1R0F Gallium-substituted rubredoxin Deposited 2003-09-22	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	GA GALLIUM (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.205
1R0G mercury-substituted rubredoxin Deposited 2003-09-22	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	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.189
1R0H cobalt-substituted rubredoxin Deposited 2003-09-22	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	CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.197
1R0I cadmium-substituted rubredoxin Deposited 2003-09-22	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	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.146
1R0J nickel-substituted rubredoxin Deposited 2003-09-22	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	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.242
1SMM Crystal Structure of Cp Rd L41A mutant in oxidized state Deposited 2004-03-09	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：L41A	SO4 SULFATE ION × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；ammonium sulfate, sodium chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.36 Å R-free 0.189
1SMU Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced) Deposited 2004-03-09	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：L41A	FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；ammonium sulfate, sodium dithionite, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.43 Å R-free 0.213
1SMW Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked) Deposited 2004-03-09	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：L41A	FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；ammonium sulfate, sodium chloride, sodium dithionite, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.38 Å R-free 0.200
1T9O Crystal Structure of V44G Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：V44G	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.00 Å R-free 0.183
1T9O Crystal Structure of V44G Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa）	Mutation：V44G	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.00 Å R-free 0.183
1T9O Crystal Structure of V44G Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–54（54 aa）	Mutation：V44G	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；ammonium sulfate, acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.00 Å R-free 0.183
1T9P Crystal Structure of V44A, G45P Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：V44A, G45P	FE FE (III) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.215
1T9P Crystal Structure of V44A, G45P Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa）	Mutation：V44A, G45P	FE FE (III) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.215
1T9P Crystal Structure of V44A, G45P Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–54（54 aa）	Mutation：V44A, G45P	FE FE (III) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.215
1T9Q Crystal Structure of V44L Cp Rubredoxin Deposited 2004-05-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：V44L	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；ammonium sulfate, acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.228
2PVE NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-09	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：K7T,I8V,I41L,A44V,P45G,S47D,E48Q	ZN ZINC ION × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；298 K；48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50	Resolution 0.79 Å R-free 0.125
2PVE NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-09	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：K7T,I8V,I41L,A44V,P45G,S47D,E48Q	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；298 K；48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50	Resolution 0.79 Å R-free 0.125
2PVE NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin Deposited 2007-05-09	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：K7T,I8V,I41L,A44V,P45G,S47D,E48Q	ZN ZINC ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；298 K；48% Ammonium Sulphate, 3% Ethanol Glycol, 0.1M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.50	Resolution 0.79 Å R-free 0.125
4MBS Crystal Structure of the CCR5 Chemokine Receptor Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa） Fragment：Rubredoxin inserted into CCR5 between residue 223 and 227	Mutation：C58Y, G163N, A233D, K303E	MRV 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide × 1 ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；32% PEG 400, 0.1M HEPES, 0.1M sodium chloride, pH 7.0, Lipidic cubic phase, temperature 293K	Resolution 2.71 Å R-free 0.263
4MBS Crystal Structure of the CCR5 Chemokine Receptor Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa） Fragment：Rubredoxin inserted into CCR5 between residue 223 and 227	Mutation：C58Y, G163N, A233D, K303E	MRV 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide × 1 ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；32% PEG 400, 0.1M HEPES, 0.1M sodium chloride, pH 7.0, Lipidic cubic phase, temperature 293K	Resolution 2.71 Å R-free 0.263
4XNV The human P2Y1 receptor in complex with BPTU Deposited 2015-01-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：D320N	BUR 1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea × 1 CLR CHOLESTEROL × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 1PE PENTAETHYLENE GLYCOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG2000MME Sodium Citrate	Resolution 2.20 Å R-free 0.230
4XNW The human P2Y1 receptor in complex with MRS2500 Deposited 2015-01-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：D320N	2ID [(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG400 Sodium citrate HEPES	Resolution 2.70 Å R-free 0.267
4XNW The human P2Y1 receptor in complex with MRS2500 Deposited 2015-01-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–54（54 aa）	Mutation：D320N	2ID [(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG400 Sodium citrate HEPES	Resolution 2.70 Å R-free 0.267
5RXN COMBINED CRYSTALLOGRAPHIC REFINEMENT AND ENERGY MINIMIZATION OF RUBREDOXIN AT 1.2 ANGSTROM RESOLUTION Deposited 1984-10-15	Parsed fields agree	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 mmCIF provides none of the parsed conditions	Resolution 1.20 Å
5UIW Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5 Deposited 2017-01-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–54（54 aa）	Mutation：C58Y, G163N, A233D, K303E	ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 OLA OLEIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.3；295.5 K；29% (v/v) PEG 400, 120 mM lithium citrate, 1.2% (w/v) 1,5-Diaminopentane dihydrochloride, 100 mM 2-(N-morpholino)ethanesulfonic acid	Resolution 2.20 Å R-free 0.250
5VBL Structure of apelin receptor in complex with agonist peptide Deposited 2017-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–54（54 aa） Fragment：UNP residues 7-229, UNP residues 1-54, UNP residues 243-330	Mutation：V117A, T177N,W261K, C325L, C326M	ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM MES pH 6.1, 26% PEG500 DME, 125mM MgCl2, 100mM NaCl, 500uM AMG3054	Resolution 2.60 Å R-free 0.256
6AKX The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21 Deposited 2018-09-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：C58Y, G163N, A233D, K303E	ZN ZINC ION × 1 NO3 NITRATE ION × 1 A4R N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-2-yl)propyl]cyclopentanecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；PEG 400, HEPES pH 7.5, ammonium acetate	Resolution 2.80 Å R-free 0.269
6AKX The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21 Deposited 2018-09-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa）	Mutation：C58Y, G163N, A233D, K303E	ZN ZINC ION × 1 NO3 NITRATE ION × 1 A4R N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-2-yl)propyl]cyclopentanecarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；PEG 400, HEPES pH 7.5, ammonium acetate	Resolution 2.80 Å R-free 0.269
6AKY The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34 Deposited 2018-09-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：C58Y, G163N, A233D, K303E	ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 A4X 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；PEG400, HEPES, ammonium acetate	Resolution 2.80 Å R-free 0.283
6BD4 Crystal structure of human apo-Frizzled4 receptor Deposited 2017-10-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：M309L, C450I, C507F, S508Y	ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 OLA OLEIC ACID × 5 SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium cacodylate trihydrate (pH 6.0), 80 mM Magnesium Sulfate, 30% PEG400, 1.5-2.5% v/v (+/-)-2-Methyl-2,4-pentanediol	Resolution 2.40 Å R-free 0.233
6GPS CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812 Deposited 2018-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa） Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ;	Mutation：;N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E,N14Q, C70Y, G175N, A241D, K311E ;	ZN ZINC ION × 1 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；reconstituted into lipidic cubic phase (LCP) by mixing with 9.9 MAG (Monoolein, Sigma) using a syringe mixer as described previously (Caffrey and Cherezov, 2009). 35 % (w/w) of the receptor solution was mixed with 61.5 % monoolein (w/w), additionally supplemented with 3.5 % cholesterol (w/w). Crystallization trials were performed in 96-well glass sandwich plates (Molecular Dimensions). The LCP drops were pipetted in a bolus volume of 50 nl using a gryphon robot and overlaid with 800 nl of precipitant solution per well. Diffracting quality crystals were obtained with 0.1 M MES pH 6.0, 0.2 M ammonium acetate and 40 % PEG400	Resolution 3.30 Å R-free 0.296
6GPX CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812 Deposited 2018-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa） Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ;	Not recorded	ZN ZINC ION × 1 OLA OLEIC ACID × 11 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.5；293 K；protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol	Resolution 2.70 Å R-free 0.243
6GPX CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812 Deposited 2018-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa） Fragment：;RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235,RUBREDOXIN INSERTED INTO CCR2A BETWEEN RESIDUE 231 AND 235 ;	Not recorded	OLA OLEIC ACID × 3 F7N [(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.5；293 K；protein was concentrated to 20-25 mg/ml and reconstituted into LCP by mixing with 90% monoolein/10% cholesterol at a 40:60 (w:w) protein:lipid ratio. LCP crystallization were set up using the IMISX in-situ crystallization plate. 40nl of LCP bolus were dispensed using the Mosquito LCP robot (TTP Labtech) and overlaid with 800 nl of precipitant solution. Crystals were obtained in 0.1 M bis-tris propane pH 6.5, 0.2 M potassium nitrate, 39% (v/v) PEG400, 3% (v/v) 1,2-propanediol	Resolution 2.70 Å R-free 0.243
6IIU Crystal structure of the human thromboxane A2 receptor bound to ramatroban Deposited 2018-10-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：M1007W/H1102I/R1106L/L247A	A8X 3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid × 1 ZN ZINC ION × 1 CLR CHOLESTEROL × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；Magnesium acetate, PEG 500 DME	Resolution 2.50 Å R-free 0.218
6IIV Crystal structure of the human thromboxane A2 receptor bound to daltroban Deposited 2018-10-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：M1007W/H1102I/R1106L/L247A	A90 2-[4-[2-[(4-chlorophenyl)sulfonylamino]ethyl]phenyl]ethanoic acid × 1 ZN ZINC ION × 1 CLR CHOLESTEROL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；Magnesium acetate, PEG 400	Resolution 3.00 Å R-free 0.237
6KNM Apelin receptor in complex with single domain antibody Deposited 2019-08-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–54（54 aa）	Mutation：V117A, T177N,W261K, C325L, C326M,V117A, T177N,W261K, C325L, C326M,V117A, T177N,W261K, C325L, C326M	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES pH 6.1, 26% PEG500 DME, 125 mM MgCl2, 100 mM NaCl	Resolution 3.20 Å R-free 0.305
6LI2 Crystal structure of GPR52 ligand free form with rubredoxin fusion Deposited 2019-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–54（53 aa）	Mutation：W278Q, C314P, S318A, N321D, V323T	ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 11 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；0.08-0.1 M magnesium sulphate, 0.1 M sodium cacodylate trihydrate pH 6.2, and 28-31% PEG300	Resolution 2.80 Å R-free 0.263
6LN2 Crystal structure of full length human GLP1 receptor in complex with Fab fragment (Fab7F38) Deposited 2019-12-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–54（54 aa）	Mutation：S193C,I196F,S225A,M233C,S271A,I317C,G318I,K346A,C347F,G361C,E387D	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 97Y N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；200-300 mM Ammonium formate, 36% PEG 400, 5%-10% (w/v) Guanidine hydrochloride	Resolution 3.20 Å R-free 0.262
6ME6 XFEL crystal structure of human melatonin receptor MT2 in complex with 2-phenylmelatonin Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 2 ZN ZINC ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 2.80 Å R-free 0.249
6ME7 XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 3.20 Å R-free 0.250
6ME7 XFEL crystal structure of human melatonin receptor MT2 (H208A) in complex with 2-phenylmelatonin Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 3.20 Å R-free 0.250
6ME8 XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 3.10 Å R-free 0.262
6ME8 XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 3.10 Å R-free 0.262
6ME9 XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 3.30 Å R-free 0.270
6ME9 XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon Deposited 2018-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–53（53 aa）	Mutation：M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P	JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate	Resolution 3.30 Å R-free 0.270
7F1T Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a Deposited 2021-06-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：T15C,T108C,C150Y,M156A,G255N,A376D,R417A,T427A,K446E	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM HEPES, pH 6.0, 250mM ammonium sulfate, 30% (v/v) PEG 400, 8% (v/v) PPG 400	Resolution 2.60 Å R-free 0.271
7SUS Crystal structure of Apelin receptor in complex with small molecule Deposited 2021-11-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：V117A,E174C,T177N,M217C,I250C,C325L,C326M	ZN ZINC ION × 1 8EH (1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM MES pH 6.1, 26% PEG500 DME, 125 mM MgCl2, 100 mM NaCl	Resolution 2.70 Å R-free 0.274

44 other PDB entries and 58 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RUBR_CLOPA
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	4rxn
Deposition date deposition_date	1984-10-15
Structure title title	CRYSTALLOGRAPHIC REFINEMENT OF RUBREDOXIN AT 1.2 ANGSTROMS RESOLUTION
Keywords keywords	ELECTRON TRANSFER(IRON-SULFUR PROTEIN); ELECTRON TRANSFER(IRON-SULFUR PROTEIN)
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	11.62 Å
Radius of gyration Rg (electron density) rg_electron	10.07 Å
Forward intensity I(0) i0	988684.00
Molecular weight molecular_weight	6094.0 kDa
Excluded volume excluded_volume	7386 Å³
Envelope volume envelope_volume	8141 Å³
Hydration-shell volume shell_volume	7142 Å³
Envelope diameter envelope_diameter	33.8 Å
Shell Rg shell_rg	15.20 Å
Envelope Rg envelope_rg	10.43 Å
Shape Rg shape_rg	10.03 Å
Total Rg total_rg	11.58 Å
Total atoms total_atoms	757
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	35.7 Å
Rg (real space) rg_real	11.53 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	9.8870e+05
I(0) uncertainty (real space) i0_real_error	1.0710e+04
Rg (reciprocal space) rg_reciprocal	11.54 Å
I(0) (reciprocal space) i0_reciprocal	988700.0000
Solution quality estimate total_estimate	0.8957
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.077
Kurtosis Kurtosis kurtosis	-0.330
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	112800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RUBREDOXIN
Molecular weight formula_weight	6054.6 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	884

MKKYTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVGKDEFEEVEE

来源 Source

来源生物 organism	Clostridium pasteurianum
NCBI Class编号 ncbi_taxonomy_id	1501

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4rxna_
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	4rxnA00
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 (8)

Crystallographic refinement of rubredoxin at 1 x 2 A degrees resolution.

J.Mol.Biol. (1980)

PMID: 7411618 · DOI: 10.1016/S0022-2836(80)80020-9 PRIMARY

The Structure of Rubredoxin at 1.2 Angstroms Resolution

J.Mol.Biol. (1979)

Water Structure in a Protein Crystal. Rubredoxin at 1.2 Angstroms Resolution.

J.Mol.Biol. (1978)

Refinement of the Model of a Protein. Rubredoxin at 1.5 Angstroms Resolution

Acta Crystallogr.,Sect.B (1973)

Sequence of Rubredoxin by X-Ray Diffraction

J.Mol.Biol. (1973)

The Structure of a Non-Heme Iron Protein, Rubredoxin at 1.5 Angstroms Resolution

Cold Spring Harbor Symp.Quant.Biol. (1972)

The Primary Structure of Clostridium Pasteurianum Rubredoxin

Thesis (1972)

Structure of Rubredoxin. An X-Ray Study to 2.5 Angstroms Resolution

J.Mol.Biol. (1970)

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Unit-cell length a length_a	64.290 Å
Unit-cell length b length_b	64.290 Å
Unit-cell length c length_c	32.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1280
R_free r_free	—

fit	/app/data/saxs_computation/rx/4rxn/4rxn.fit
pddf	/app/data/pr_computation/rx/4rxn/4rxn.pr.out
profile	/app/data/saxs_computation/rx/4rxn/4rxn.dat