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3h56

Met150Leu/Phe312Cys variant of nitrite reductase from Alcaligenes faecalis

Method: X-RAY DIFFRACTION Dmax: 76.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Copper-containing nitrite reductase

Alcaligenes faecalis

UniProt P38501

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 40–375 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

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 3H56 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 mutation/modification 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 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）
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 mutation/modification 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 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）
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 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 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 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）
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 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）
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 mutation/modification 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 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 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 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）
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 mutation/modification 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 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）
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 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）
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 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）
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 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）
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 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）
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 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 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
4YSC Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis Deposited 2015-03-17 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：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 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：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
5D4H High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography Deposited 2015-08-07 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：UNP residue 40-376
Chain B 40–376（337 aa） Fragment：UNP residue 40-376
Chain C 40–376（337 aa） Fragment：UNP residue 40-376
Not recorded 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
5D4I Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography Deposited 2015-08-07 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：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 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：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 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）
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 mutation/modification 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 1–336； UniProt 40–375

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3h56

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3h56
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3h56
Deposition date deposition_date2009-04-21
Structure title titleMet150Leu/Phe312Cys variant of nitrite reductase from Alcaligenes faecalis
Keywords keywords;nitrite reductase, high-throughput screening, oxidase, copper, FAD, Flavoprotein, Metal-binding, Nitrate assimilation, Oxidoreductase, Periplasm, Pyrrolidone carboxylic acid ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.70 Å
Radius of gyration Rg (electron density) rg_electron20.66 Å
Forward intensity I(0) i022587600.00
Molecular weight molecular_weight36347.0 kDa
Excluded volume excluded_volume45471 ų
Envelope volume envelope_volume53591 ų
Hydration-shell volume shell_volume21754 ų
Envelope diameter envelope_diameter83.2 Å
Shell Rg shell_rg27.45 Å
Envelope Rg envelope_rg21.46 Å
Shape Rg shape_rg20.64 Å
Total Rg total_rg21.63 Å
Total atoms total_atoms2559
Residues n_residues335
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.5 Å
Rg (real space) rg_real21.70 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real2.2590e+07
I(0) uncertainty (real space) i0_real_error2.9860e+05
Rg (reciprocal space) rg_reciprocal21.70 Å
I(0) (reciprocal space) i0_reciprocal22590000.0000
Solution quality estimate total_estimate0.7729
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness0.394
Kurtosis Kurtosis kurtosis-0.149
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5288000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3h56a1
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.0 — automated matches
Domain ID domain_idd3h56a2
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3h56A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3h56A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
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8. Citations (1)

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9. Files and Curves (10)