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2vm4

Structure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2

Method: X-RAY DIFFRACTION Dmax: 82.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

ACHROMOBACTER XYLOSOXIDANS

UniProt O68601

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 25–360 Fragment：RESIDUES 25-360 CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5 Resolution 1.90 Å R-free 0.214

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 2VM4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BQ5 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051 Deposited 1998-08-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 19–360（342 aa）
Not recorded CU COPPER (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.05 Å R-free 0.226
1GS6 Crystal structure of M144A mutant of Alcaligenes xylosoxidans Nitrite Reductase Deposited 2002-01-02 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 X 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG 4000, 0.1M MGCL2, 0.1M TRIS-HCL PH8.5, TEMP GRADIENT 4-32 DEGREES C, pH 8.50
Resolution 2.20 Å R-free 0.181
1GS7 Crystal structure of H254F mutant of Alcaligenes xylosoxidans Nitrite Reductase Deposited 2002-01-02 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 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 3 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；40-50% PEG-MME 550, 10MM ZNSO4, 0.1M MES PH6.5, pH 6.50
Resolution 1.85 Å R-free 0.194
1GS8 Crystal structure of mutant D92N Alcaligenes xylosoxidans Nitrite Reductase Deposited 2002-01-02 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 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.5；40-50% PEG-MME 550, 10MM ZNSO4, 0.1M MES PH 6.5
Resolution 1.90 Å R-free 0.207
1HAU X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION Deposited 2001-04-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa）
Not recorded CU COPPER (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG 4K, 0.1M MAGNESIUM CHLORIDE, 0.1M TRIS-HCL PH8.5, pH 8.50
Resolution 1.90 Å R-free 0.190
1HAW X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION Deposited 2001-04-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa）
Not recorded CU1 COPPER (I) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% PEG 4K, 0.1M MAGNESIUM CHLORIDE, 0.1M TRIS-HCL PH8.5, pH 8.50
Resolution 1.90 Å R-free 0.199
1NDT NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS Deposited 1998-10-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 26–359（334 aa）
Not recorded CU COPPER (II) ION × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.60
Resolution 2.10 Å R-free 0.208
1OE1 Atomic Resolution Structure of the Wildtype Native Nitrite Reductase from Alcaligenes xylosoxidans Deposited 2003-03-18 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 25–360（336 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 6 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；40-50% PEG-MME 550, 0.1M MES PH 6.5, 10MM CUSO4
Resolution 1.04 Å R-free 0.142
1OE2 Atomic Resolution Structure of D92E Mutant of Alcaligenes xylosoxidans Nitrite Reductase Deposited 2003-03-18 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 25–360（336 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 6 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1M MES PH6.5 40-50% PEG-MME 550, 10MM CUSO4,, pH 6.50
Resolution 1.12 Å R-free 0.179
1OE3 Atomic resolution structure of 'Half Apo' NiR Deposited 2003-03-18 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 25–360（336 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 6 PG4 TETRAETHYLENE GLYCOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；40% PEG MME 550, 0.1M MES PH 6.5, 10MM ZNSO4
Resolution 1.15 Å R-free 0.148
1WA0 Crystal Structure Of W138H Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase Deposited 2004-10-22 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 X 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 6 SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；CRYSTALS OF TRP138HIS NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY.
Resolution 1.60 Å R-free 0.192
1WA1 Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase Deposited 2004-10-22 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 X 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 3 SO4 SULFATE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY.
Resolution 1.65 Å R-free 0.191
1WA2 Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase with nitrite bound Deposited 2004-10-22 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 X 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 6 NO2 NITRITE ION × 3 SO4 SULFATE ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY. FOR HIS313GLN_NO2.-, 10MM SODIUM NITRITE WAS ADDED TO THE RESERVOIR SOLUTION PRIOR TO CRYSTALLISATION.
Resolution 1.72 Å R-free 0.210
1WAE Crystal structure of H129V Mutant of Alcaligenes Xylosoxidans Nitrite Reductase Deposited 2004-10-26 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 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；100MM MES BUFFER PH 6.5 200MM ZNSO4, 40-50% PEG550 MME
Resolution 1.95 Å R-free 0.226
2BO0 Crystal structure of the C130A mutant of nitrite reductase from Alcaligenes xylosoxidans Deposited 2005-04-06 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 25–360（336 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 9 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PEG 550 MME, ZNSO4, MES PH 6.5
Resolution 1.35 Å R-free 0.113
2BP0 M144L mutant of nitrite reductase from Alcaligenes xylosoxidans Deposited 2005-04-17 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 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 18 SO4 SULFATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.196
2BP0 M144L mutant of nitrite reductase from Alcaligenes xylosoxidans Deposited 2005-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 15 SO4 SULFATE ION × 9 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.196
2BP8 M144Q Structure of nitrite reductase from Alcaligenes xylosoxidans Deposited 2005-04-18 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 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 15 SO4 SULFATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.189
2BP8 M144Q Structure of nitrite reductase from Alcaligenes xylosoxidans Deposited 2005-04-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 25–360（336 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 15 SO4 SULFATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.189
2JFC M144L mutant of Nitrite Reductase from Alcaligenes xylosoxidans in space group P212121 Deposited 2007-01-31 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 26–360（335 aa） Fragment：RESIDUES 26-360
Chain D 26–360（335 aa） Fragment：RESIDUES 26-360
Chain E 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES Mutation：YES Mutation：YES CU COPPER (II) ION × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；pH 4.20
Resolution 2.40 Å R-free 0.193
2JFC M144L mutant of Nitrite Reductase from Alcaligenes xylosoxidans in space group P212121 Deposited 2007-01-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 26–360（335 aa） Fragment：RESIDUES 26-360
Chain C 26–360（335 aa） Fragment：RESIDUES 26-360
Chain F 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES Mutation：YES Mutation：YES CU COPPER (II) ION × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.2；pH 4.20
Resolution 2.40 Å R-free 0.193
2VM3 Structure of Alcaligenes xylosoxidans in space group R3 - 1 of 2 Deposited 2008-01-22 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.80 Å R-free 0.210
2VMJ Type 1 Copper-Binding Loop of Nitrite Reductase mutant: 130- CAPEGMVPWHVVSGM-144 to 130-CTPHPFM-136 Deposited 2008-01-28 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 25–154（130 aa） Fragment：RESIDUES 25-154,168-360
Chain A 168–360（193 aa） Fragment：RESIDUES 25-154,168-360
Not recorded ZN ZINC ION × 9 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；50 MM HEPES PH 7.0, 5 MM ZNCL2 AND 10 % PEG 6000
Resolution 2.50 Å R-free 0.232
2VN3 Nitrite Reductase from Alcaligenes xylosoxidans Deposited 2008-01-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；100 MM MES PH 6.5, 10 MM ZNSO4 AND 25 % PEG-MME 550
Resolution 2.35 Å R-free 0.215
2VW4 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 2 OF 3 Deposited 2008-06-16 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.90 Å R-free 0.197
2VW4 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 2 OF 3 Deposited 2008-06-16 Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.90 Å R-free 0.197
2VW6 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 3 OF 3 Deposited 2008-06-16 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.90 Å R-free 0.194
2VW6 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 3 OF 3 Deposited 2008-06-16 Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.90 Å R-free 0.194
2VW7 Nitrite reductase from Alcaligenes xylosoxidans - 1 of 3 Deposited 2008-06-16 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5
Resolution 1.90 Å R-free 0.201
2VW7 Nitrite reductase from Alcaligenes xylosoxidans - 1 of 3 Deposited 2008-06-16 Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 25–360（336 aa） Fragment：RESIDUES 25-360
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5
Resolution 1.90 Å R-free 0.201
2XWZ STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite Deposited 2010-11-06 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 26–360（335 aa） Fragment：RESIDUES 26-360
Chain D 26–360（335 aa） Fragment：RESIDUES 26-360
Chain E 26–360（335 aa） Fragment：RESIDUES 26-360
Not recorded CU COPPER (II) ION × 6 NO2 NITRITE ION × 2 SO4 SULFATE ION × 23 ACT ACETATE ION × 6 NO NITRIC OXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.25；1.8 M LITHIUM SULFATE, 100MM ACETATE BUFFER PH 4.25
Resolution 2.34 Å R-free 0.199
2XWZ STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite Deposited 2010-11-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 26–360（335 aa） Fragment：RESIDUES 26-360
Chain C 26–360（335 aa） Fragment：RESIDUES 26-360
Chain F 26–360（335 aa） Fragment：RESIDUES 26-360
Not recorded CU COPPER (II) ION × 6 NO2 NITRITE ION × 2 SO4 SULFATE ION × 21 ACT ACETATE ION × 5 NO NITRIC OXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.25；1.8 M LITHIUM SULFATE, 100MM ACETATE BUFFER PH 4.25
Resolution 2.34 Å R-free 0.199
2XX0 STRUCTURE OF THE N90S-H254F MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS Deposited 2010-11-07 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 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 9 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；ZNSO4, PEG 550 MME, MES PH 6.5
Resolution 1.46 Å R-free 0.151
2XX0 STRUCTURE OF THE N90S-H254F MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS Deposited 2010-11-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 9 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；ZNSO4, PEG 550 MME, MES PH 6.5
Resolution 1.46 Å R-free 0.151
2XX1 STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite Deposited 2010-11-07 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 26–360（335 aa） Fragment：RESIDUES 26-360
Chain D 26–360（335 aa） Fragment：RESIDUES 26-360
Chain E 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES Mutation：YES Mutation：YES CU COPPER (II) ION × 6 NO2 NITRITE ION × 3 SO4 SULFATE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；1.8 M AMMONIUM SULPHATE IN CITRATE BUFFER, PH 4.6
Resolution 3.00 Å R-free 0.221
2XX1 STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite Deposited 2010-11-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 26–360（335 aa） Fragment：RESIDUES 26-360
Chain C 26–360（335 aa） Fragment：RESIDUES 26-360
Chain F 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES Mutation：YES Mutation：YES CU COPPER (II) ION × 6 NO2 NITRITE ION × 3 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；1.8 M AMMONIUM SULPHATE IN CITRATE BUFFER, PH 4.6
Resolution 3.00 Å R-free 0.221
2XXF Cu metallated H254F mutant of nitrite reductase Deposited 2010-11-10 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 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 9 PEG DI(HYDROXYETHYL)ETHER × 9 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PEG 550 MME, ZNSO4, MES PH 6.5
Resolution 1.50 Å R-free 0.176
2XXF Cu metallated H254F mutant of nitrite reductase Deposited 2010-11-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 26–360（335 aa） Fragment：RESIDUES 26-360
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 9 PEG DI(HYDROXYETHYL)ETHER × 12 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PEG 550 MME, ZNSO4, MES PH 6.5
Resolution 1.50 Å R-free 0.176
2XXG STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS Deposited 2010-11-10 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 26–360（335 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PG4 TETRAETHYLENE GLYCOL × 3 CU COPPER (II) ION × 6 ZN ZINC ION × 6 PEG DI(HYDROXYETHYL)ETHER × 6 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PEG 550 MME, ZNSO4, MES PH 6.5.
Resolution 1.60 Å R-free 0.211
2XXG STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS Deposited 2010-11-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain C 26–360（335 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) PG4 TETRAETHYLENE GLYCOL × 3 CU COPPER (II) ION × 6 ZN ZINC ION × 6 PEG DI(HYDROXYETHYL)ETHER × 6 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PEG 550 MME, ZNSO4, MES PH 6.5.
Resolution 1.60 Å R-free 0.211
2ZON Crystal structure of electron transfer complex of nitrite reductase with cytochrome c Deposited 2008-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–360（336 aa） Fragment：UNP residues 25-360
Chain B 25–360（336 aa） Fragment：UNP residues 25-360
Chain C 25–360（336 aa） Fragment：UNP residues 25-360
Not recorded CU COPPER (II) ION × 6 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；PEG 3350, Magnesium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.70 Å R-free 0.195
4CSP Structure of the F306C mutant of nitrite reductase from Achromobacter xylosoxidans Deposited 2014-03-09 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain F 26–360（335 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 12 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.70 Å R-free 0.215
4CSP Structure of the F306C mutant of nitrite reductase from Achromobacter xylosoxidans Deposited 2014-03-09 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 26–360（335 aa）
Mutation：YES CU COPPER (II) ION × 6 ZN ZINC ION × 9 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.70 Å R-free 0.215
4CSZ STRUCTURE OF F306C MUTANT OF NITRITE REDUCTASE FROM Achromobacter XYLOSOXIDANS WITH NITRITE BOUND Deposited 2014-03-11 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 26–360（335 aa）
Mutation：YES ZN ZINC ION × 21 CU COPPER (II) ION × 6 NO2 NITRITE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；15% PEG550 MME, 50 MM ZNSO4, AND 50 MM MES BUFFER, pH 6.5
Resolution 1.75 Å R-free 0.210
5B1J Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa） Fragment：UNP residues 25-360
Chain B 25–360（336 aa） Fragment：UNP residues 25-360
Not recorded CU COPPER (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, potassium chloride
Resolution 3.00 Å R-free 0.233
5B1K Crystal structure of the chloride-bound form of blue copper nitrite reductase Deposited 2015-12-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–360（336 aa）
Not recorded CU COPPER (II) ION × 6 CL CHLORIDE ION × 3 PG4 TETRAETHYLENE GLYCOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；293 K；PEG 3350, Sodium Chloride, Magnesium Chloride
Resolution 1.35 Å R-free 0.173
5ONX Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography Deposited 2017-08-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 26–360（335 aa）
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 OXY OXYGEN MOLECULE × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；10% w/v PEG 550 MME, 10 mM ZnSO4, 100 mM MES buffer pH 6.5
Resolution 1.60 Å R-free 0.226
5ONY As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans Deposited 2017-08-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 26–360（335 aa）
Not recorded CU COPPER (II) ION × 6 ZN ZINC ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；10% w/v PEG 550 MME, 10 mM ZnSO4, 100 mM MES buffer, pH 6.5
Resolution 1.60 Å R-free 0.223

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

View Construct and Data Evidence
UniProt name O68601_ALCXX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–336； UniProt 25–360

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 2vm4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2vm4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2vm4
Deposition date deposition_date2008-01-22
Structure title titleStructure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2
Keywords keywordsDENITRIFICATION, NITRITE REDUCTASE, OXIDOREDUCTASE, ORDERED MECHANISM; 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_guinier21.56 Å
Radius of gyration Rg (electron density) rg_electron20.86 Å
Forward intensity I(0) i023001500.00
Molecular weight molecular_weight36527.0 kDa
Excluded volume excluded_volume45673 ų
Envelope volume envelope_volume54962 ų
Hydration-shell volume shell_volume22032 ų
Envelope diameter envelope_diameter84.9 Å
Shell Rg shell_rg27.56 Å
Envelope Rg envelope_rg21.96 Å
Shape Rg shape_rg20.84 Å
Total Rg total_rg21.80 Å
Total atoms total_atoms2566
Residues n_residues334
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 dmax82.9 Å
Rg (real space) rg_real21.58 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real2.3000e+07
I(0) uncertainty (real space) i0_real_error3.1750e+05
Rg (reciprocal space) rg_reciprocal21.57 Å
I(0) (reciprocal space) i0_reciprocal23000000.0000
Solution quality estimate total_estimate0.8004
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.4 Å
Skewness Skewness skewness0.447
Kurtosis Kurtosis kurtosis0.033
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6126000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.533; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2vm4a1
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.3 — Multidomain cupredoxins
Domain ID domain_idd2vm4a2
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.3 — Multidomain cupredoxins

CATH v4.4 (2 domains)

Domain ID domain_id2vm4A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2vm4A02
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)