5ony

As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans

Method: X-RAY DIFFRACTION D_max: 88.2 Å Quality: GOOD

▼

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

Copper-containing nitrite reductase

Alcaligenes xylosoxydans xylosoxydans

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 26–360	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

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 5ONY	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 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） 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
2VM4 Structure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2 Deposited 2008-01-22	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） 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 0.214
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 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） 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 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） 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 construct 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） 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 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） 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 construct 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） 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 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） 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 construct 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） 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 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 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 mutation/modification Different ligand/ion Different experimental conditions 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 mutation/modification Different ligand/ion Different experimental conditions 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 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 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

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 1–335； UniProt 26–360

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

P(r) Distance Distribution P(r) Distribution

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ony
Deposition date deposition_date	2017-08-04
Structure title title	As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans
Keywords keywords	Copper Ion Binding, Oxidoreductase Activity, Metal Ion Binding, Nitrite Reductase Activity, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.97 Å
Radius of gyration Rg (electron density) rg_electron	21.24 Å
Forward intensity I(0) i0	23934400.00
Molecular weight molecular_weight	37171.0 kDa
Excluded volume excluded_volume	46424 Å³
Envelope volume envelope_volume	56245 Å³
Hydration-shell volume shell_volume	22263 Å³
Envelope diameter envelope_diameter	92.3 Å
Shell Rg shell_rg	27.80 Å
Envelope Rg envelope_rg	22.54 Å
Shape Rg shape_rg	21.19 Å
Total Rg total_rg	22.24 Å
Total atoms total_atoms	2607
Residues n_residues	335
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

▼

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

Maximum dimension Dmax dmax	88.2 Å
Rg (real space) rg_real	22.04 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	2.3930e+07
I(0) uncertainty (real space) i0_real_error	3.1990e+05
Rg (reciprocal space) rg_reciprocal	22.03 Å
I(0) (reciprocal space) i0_reciprocal	23930000.0000
Solution quality estimate total_estimate	0.7605
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.544
Kurtosis Kurtosis kurtosis	0.303
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6847000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.430; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.602; Smooth: 0.991

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Copper-containing nitrite reductase
Molecular weight formula_weight	36442.4 kDa
EC 编号 ec_number	1.7.2.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2996

DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR

来源 Source

来源生物 organism	Alcaligenes xylosoxydans xylosoxydans
NCBI Class编号 ncbi_taxonomy_id	85698
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	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	378

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5onya1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d5onya2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

CATH v4.4 (2 domains)

Domain ID domain_id	5onyA01
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	5onyA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

▶

8. Citations (1)

▶

Unit-cell length a length_a	90.347 Å
Unit-cell length b length_b	90.347 Å
Unit-cell length c length_c	143.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	47.860 Å
R factor r_factor	0.1914
R_work r_work	0.1896
R_free r_free	0.2233

fit	/app/data/saxs_computation/on/5ony/5ony.fit
pddf	/app/data/pr_computation/on/5ony/5ony.pr.out
profile	/app/data/saxs_computation/on/5ony/5ony.dat