5d4h

High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography

Method: X-RAY DIFFRACTION D_max: 84.2 Å Quality: EXCELLENT

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

Copper-containing nitrite reductase

Alcaligenes faecalis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 40–376 Chain B； UniProt 40–376 Chain C； UniProt 40–376	Fragment：UNP residue 40-376	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3 GOL GLYCEROL × 22 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；100mM sodium acetate (pH 4.1) and 7% PEG 4000	Resolution 1.30 Å R-free 0.165

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 5D4H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AQ8 STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE REDUCED WITH ASCORBATE Deposited 1997-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Not recorded	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；10% PEG4000, 0.1 SODIUM ACETATE PH 4.5	Resolution 2.00 Å
1AS6 STRUCTURE OF NITRITE BOUND TO OXIDIZED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE Deposited 1997-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Not recorded	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；10% PEG4000, 0.1 SODIUM ACETATE PH 4.5	Resolution 1.80 Å
1AS7 STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE Deposited 1997-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Not recorded	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；10% PEG4000, 0.1 SODIUM ACETATE PH 4.5	Resolution 2.00 Å
1AS8 STRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE Deposited 1997-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Not recorded	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；10% PEG4000, 0.1 SODIUM ACETATE PH 4.5	Resolution 1.85 Å
1ET5 CRYSTAL STRUCTURE OF NITRITE REDUCTASE ASP98ASN MUTANT FROM ALCALIGENES FAECALIS S-6 Deposited 2000-04-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：40 - 376	Mutation：D98N	CU COPPER (II) ION × 6 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；sodium cacodylate, zinc acetate, PEG 4000, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.214
1ET7 CRYSTAL STRUCTURE OF NITRITE REDUCTASE HIS255ASP MUTANT FROM ALCALIGENES FAECALIS S-6 Deposited 2000-04-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：40 - 376	Mutation：H255D	CU COPPER (II) ION × 6 CD CADMIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；PEG 6000 sodium cacodylate, cadmium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.210
1ET8 CRYSTAL STRUCTURE OF NITRITE REDUCTASE HIS255ASN MUTANT FROM ALCALIGENES FAECALIS Deposited 2000-04-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：40 - 376	Mutation：H255N	CU COPPER (II) ION × 6 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；PEG 8000, sodium cacodylate, zinc acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.212
1J9Q Crystal structure of nitrite soaked oxidized D98N AFNIR Deposited 2001-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：Residues 40-376 Chain B 40–376（337 aa） Fragment：Residues 40-376 Chain C 40–376（337 aa） Fragment：Residues 40-376	Mutation：D98N Mutation：D98N Mutation：D98N	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium acetate, sodium nitrite, copper chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.210
1J9R Crystal structure of nitrite soaked reduced D98N AFNIR Deposited 2001-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：D98N Mutation：D98N Mutation：D98N	CU COPPER (II) ION × 9 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium acetate, sodium nitrite, copper chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.225
1J9S Crystal structure of nitrite soaked oxidized H255N AFNIR Deposited 2001-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：H255N Mutation：H255N Mutation：H255N	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium acetate, copper chloride, sodium nitrite, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.204
1J9T Crystal structure of nitrite soaked reduced H255N AFNIR Deposited 2001-05-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：H255N Mutation：H255N Mutation：H255N	CU COPPER (II) ION × 9 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium acetate, sodium nitrite, copper chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.218
1L9O CRYSTAL STRUCTURE OF NITRITE SOAKED I257A VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：I257A Mutation：I257A Mutation：I257A	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；sodium acetate peg 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.192
1L9P CRYSTAL STRUCTURE OF NITRITE SOAKED I257G VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIES S-6 Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：I257G Mutation：I257G Mutation：I257G	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；acetate peg 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.194
1L9Q CRYSTAL STRUCTURE OF THE I257L VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6 Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：I257L Mutation：I257L Mutation：I257L	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；acetate peg 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.188
1L9R CRYSTAL STRUCTURE OF THE I257M VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6 Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：I257M Mutation：I257M Mutation：I257M	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；acetate peg 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.197
1L9S CRYSTAL STRUCTURE OF THE I257T VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6 Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：I257T Mutation：I257T Mutation：I257T	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；acetate peg 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.197
1L9T CRYSTAL STRUCTURE OF THE I257V VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6 Deposited 2002-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：RESIDUES 40-376 Chain B 40–376（337 aa） Fragment：RESIDUES 40-376 Chain C 40–376（337 aa） Fragment：RESIDUES 40-376	Mutation：I257V Mutation：I257V Mutation：I257V	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；acetate peg 4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.208
1NPJ Crystal structure of H145A mutant of nitrite reductase from Alcaligenes faecalis Deposited 2003-01-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Mutation：H145A Mutation：H145A Mutation：H145A	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；300 K；PEG 8000, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.90 Å R-free 0.225
1NPN Crystal structure of a copper reconstituted H145A mutant of nitrite reductase from Alcaligenes faecalis Deposited 2003-01-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Mutation：H145A Mutation：H145A Mutation：H145A	CU COPPER (II) ION × 6 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；300 K；PEG 8000, sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.195
1NTD STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE MUTANT M150E THAT CONTAINS ZINC Deposited 1995-07-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa）	Mutation：M150E	CU COPPER (II) ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.232
1SJM Nitrite bound copper containing nitrite reductase Deposited 2004-03-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3 ACT ACETATE ION × 5 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；PEG 4000, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 321K	Resolution 1.40 Å R-free 0.138
1SNR Nitric oxide bound to Cu nitrite reductase Deposited 2004-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 8 NO NITRIC OXIDE × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；PEG4000, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 4.0	Resolution 1.31 Å R-free 0.141
1ZDQ Crystal Structure of Met150Gly AfNiR with Methylsulfanyl Methane Bound Deposited 2005-04-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–375（336 aa） Chain B 40–375（336 aa） Chain C 40–375（336 aa）	Mutation：M150G Mutation：M150G Mutation：M150G	CU COPPER (II) ION × 6 MSM (METHYLSULFANYL)METHANE × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.199
1ZDS Crystal Structure of Met150Gly AfNiR with Acetamide Bound Deposited 2005-04-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–375（336 aa） Chain B 40–375（336 aa） Chain C 40–375（336 aa）	Mutation：M150G Mutation：M150G Mutation：M150G	CU COPPER (II) ION × 6 ACM ACETAMIDE × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å R-free 0.214
2AFN STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE AND A COPPER SITE MUTANT, M150E, THAT CONTAINS ZINC Deposited 1995-07-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Not recorded	CU COPPER (II) ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.223
2B08 Reduced acetamide-bound M150G Nitrite Reductase from Alcaligenes faecalis Deposited 2005-09-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 37–376（340 aa） Chain B 37–376（340 aa） Chain C 37–376（340 aa）	Mutation：M150G Mutation：M150G Mutation：M150G	CU1 COPPER (I) ION × 9 ACM ACETAMIDE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.220
2E86 Azide bound to copper containing nitrite reductase from A. faecalis S-6 Deposited 2007-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：residues 4-340 Chain B 40–376（337 aa） Fragment：residues 4-340 Chain C 40–376（337 aa） Fragment：residues 4-340	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 10 AZI AZIDE ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；6-8 % PEG 4000, 0.1M sodium acetate buffer pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.179
2FJS Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis Deposited 2006-01-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 10 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；8-10% PEG 4000, 0.1 M NaOAC, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.180
2P80 Solution structure of the complex between nitrite reductase and pseudoazurin from A. faecalis Deposited 2007-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU COPPER (II) ION × 7 GD GADOLINIUM ATOM × 9	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 221/223 (0.38 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 221/223 (0.38 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 234/236 (0.32 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 234/236 (0.32 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 333/336 (0.53 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 333/336 (0.53 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O	Resolution not provided
2PP7 Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound) Deposited 2007-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 13 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.180
2PP8 Formate bound to oxidized wild type AfNiR Deposited 2007-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 8 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.201
2PP9 Nitrate bound wild type oxidized AfNiR Deposited 2007-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 NO3 NITRATE ION × 3 ACT ACETATE ION × 8 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.195
2PPA Anaerobically manipulated wild type oxidized AfNiR bound to nitrous oxide Deposited 2007-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 10 N2O NITROUS OXIDE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.69 Å R-free 0.224
2PPC Oxidized wild type AfNiR exposed to NO (nitrite bound) Deposited 2007-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 NO2 NITRITE ION × 3 ACT ACETATE ION × 10 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；6-11% PEG 4000, 100mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.58 Å R-free 0.182
2PPD Oxidized H145A mutant of AfNiR bound to nitric oxide Deposited 2007-04-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Mutation：H145A Mutation：H145A Mutation：H145A	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 NO NITRIC OXIDE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；6-11% polyethylene glycol 6000, 0.1 M ammonium sulfate and 0.01 M sodium acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.212
2PPE Reduced H145A mutant of AfNiR exposed to NO Deposited 2007-04-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 34–376（343 aa） Chain B 34–376（343 aa） Chain C 34–376（343 aa）	Mutation：H145A Mutation：H145A Mutation：H145A	CU1 COPPER (I) ION × 3 CU COPPER (II) ION × 3 ACT ACETATE ION × 2 NO NITRIC OXIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；6-11% polyethylene glycol 6000, 0.1 M ammonium sulfate and 0.01 M sodium acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.196
2PPF Reduced mutant D98N of AfNiR exposed to nitric oxide Deposited 2007-04-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Mutation：D98N Mutation：D98N Mutation：D98N	CU1 COPPER (I) ION × 5 CU COPPER (II) ION × 3 ACT ACETATE ION × 8 NO NITRIC OXIDE × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；7-12% polyethylene glycol 4000, 75 mM acetamide and 10 mM sodium acetate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.170
3H4F Met62Leu variant of nitrite reductase from Alcaligenes faeclis Deposited 2009-04-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–375（336 aa） Chain B 40–375（336 aa） Chain C 40–375（336 aa）	Mutation：Met62Leu Mutation：Met62Leu Mutation：Met62Leu	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；pH 4.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.10 Å R-free 0.227
3H4H Met94Thr/Phe312Cys variant of nitrite reductase from Alcaligenes faecalis Deposited 2009-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 41–375（335 aa） Chain B 41–375（335 aa） Chain C 41–375（335 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.226
3H56 Met150Leu/Phe312Cys variant of nitrite reductase from Alcaligenes faecalis Deposited 2009-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–375（336 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；pH 4.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.50 Å R-free 0.204
4YSC Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis Deposited 2015-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：UNP residues 40-376 Chain B 40–376（337 aa） Fragment：UNP residues 40-376 Chain C 40–376（337 aa） Fragment：UNP residues 40-376	Not recorded	CU COPPER (II) ION × 6 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；293 K；100 mM sodium acetate pH 4.0, 10% PEG 4000	Resolution 2.03 Å R-free 0.203
4YSE High resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis Deposited 2015-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：UNP residues 40-376 Chain B 40–376（337 aa） Fragment：UNP residues 40-376 Chain C 40–376（337 aa） Fragment：UNP residues 40-376	Not recorded	CU COPPER (II) ION × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 ACY ACETIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；100mM sodium acetate, pH 4, 8% PEG4000	Resolution 1.20 Å R-free 0.168
5D4I Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography Deposited 2015-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：UNP residues 40-376 Chain B 40–376（337 aa） Fragment：UNP residues 40-376 Chain C 40–376（337 aa） Fragment：UNP residues 40-376	Not recorded	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 4；293 K；100mM sodium acetate (pH 4.0) and 12% PEG 4000	Resolution 1.60 Å R-free 0.196
5D4J Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals Deposited 2015-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Fragment：UNP residues 40-376 Chain B 40–376（337 aa） Fragment：UNP residues 40-376 Chain C 40–376（337 aa） Fragment：UNP residues 40-376	Not recorded	CU COPPER (II) ION × 6 CL CHLORIDE ION × 3 GOL GLYCEROL × 10 ACY ACETIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.1；293 K；1:1 mixture of the purified protein solution (40 mg/ml) and a reservoir solution composed of 100 mM sodium acetate (pH 4.1) and 7% PEG 4000	Resolution 2.00 Å R-free 0.232
5F7A Nitrite complex structure of copper nitrite reductase from Alcaligenes faecalis determined at 293 K Deposited 2015-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU COPPER (II) ION × 6 NO2 NITRITE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；100 mM sodium acetate, 7% PEG 4000	Resolution 1.54 Å R-free 0.180
5F7B Resting state structure of CuNiR form Alcaligenes faecalis determined at 293 K Deposited 2015-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 40–376（337 aa） Chain B 40–376（337 aa） Chain C 40–376（337 aa）	Not recorded	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；100 mM sodium acetate, 7% PEG 4000	Resolution 1.56 Å R-free 0.177

46 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NIR_ALCFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–338； UniProt 40–376 Author chain B； PDBConstruct 2–338； UniProt 40–376 Author chain C； PDBConstruct 2–338； UniProt 40–376

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	5d4h
Deposition date deposition_date	2015-08-07
Structure title title	High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography
Keywords keywords	copper, oxidoreductase; OXIDOREDUCTASE
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	28.77 Å
Radius of gyration Rg (electron density) rg_electron	27.80 Å
Forward intensity I(0) i0	197133000.00
Molecular weight molecular_weight	112410.0 kDa
Excluded volume excluded_volume	140720 Å³
Envelope volume envelope_volume	161560 Å³
Hydration-shell volume shell_volume	45416 Å³
Envelope diameter envelope_diameter	91.3 Å
Shell Rg shell_rg	37.37 Å
Envelope Rg envelope_rg	28.22 Å
Shape Rg shape_rg	27.76 Å
Total Rg total_rg	28.76 Å
Total atoms total_atoms	7905
Residues n_residues	1017
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	84.2 Å
Rg (real space) rg_real	28.59 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.9710e+08
I(0) uncertainty (real space) i0_real_error	2.8360e+06
Rg (reciprocal space) rg_reciprocal	28.67 Å
I(0) (reciprocal space) i0_reciprocal	197100000.0000
Solution quality estimate total_estimate	0.9073
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.8 Å
Skewness Skewness skewness	0.116
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	69090000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.909

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Copper-containing nitrite reductase
Molecular weight formula_weight	37019.9 kDa
EC 编号 ec_number	1.7.2.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9007

MATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGTLVPR

来源 Source

来源生物 organism	Alcaligenes faecalis
NCBI Class编号 ncbi_taxonomy_id	511
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	NITRITE ION
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 5 Entity 5 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	893

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5d4ha1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d5d4ha2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d5d4hb1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d5d4hb2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d5d4hb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5d4hc1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d5d4hc2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d5d4hc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	5d4hA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5d4hA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5d4hB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5d4hB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5d4hC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5d4hC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (1)

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Unit-cell length a length_a	61.419 Å
Unit-cell length b length_b	102.174 Å
Unit-cell length c length_c	145.791 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	12

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	49.510 Å
R factor r_factor	0.1253
R_work r_work	0.1232
R_free r_free	0.1648

fit	/app/data/saxs_computation/d4/5d4h/5d4h.fit
pddf	/app/data/pr_computation/d4/5d4h/5d4h.pr.out
profile	/app/data/saxs_computation/d4/5d4h/5d4h.dat