5ngx

The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite

Method: X-RAY DIFFRACTION D_max: 54.5 Å Quality: GOOD

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

;Cytochrome c' ;

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–126	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1 NO2 NITRITE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；50 mM sodium nitrite, 2.2 M ammonium sulphate and 0.1 M HEPES, pH 7.5	Resolution 1.06 Å R-free 0.200

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 5NGX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CGN CYTOCHROME C' Deposited 1995-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–127（126 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
1CGO CYTOCHROME C' Deposited 1995-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–127（126 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1E83 Cytochrome c' from Alcaligenes xylosoxidans - oxidized structure Deposited 2000-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5	Resolution 2.05 Å R-free 0.252
1E84 Cytochrome c' from Alcaligenes xylosoxidans - reduced structure Deposited 2000-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE.	Resolution 1.90 Å R-free 0.273
1E85 Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with NO bound to proximal side of heme Deposited 2000-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–127（126 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE, THEN INCUBATED FOR 6 DAYS IN MOTHER LIQUOR SATURATED WITH NO.	Resolution 1.35 Å R-free 0.220
1E86 Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with CO bound to distal side of heme Deposited 2000-09-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE, THEN INCUBATED FOR 6 DAYS IN MOTHER LIQUOR SATURATED WITH CO.	Resolution 1.95 Å R-free 0.258
2XL6 Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124A variant with bound NO Deposited 2010-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 4 NO NITRIC OXIDE × 2 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions AMMONIUM SULPHATE, TRIS PH7.5	Resolution 1.07 Å R-free 0.161
2XL8 REDUCED STRUCTURE OF R124F MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS Deposited 2010-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；SULPHATE AMMONIUM, TRIS PH 7.5	Resolution 1.14 Å R-free 0.161
2XLD Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124Q variant Deposited 2010-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；AMMONIUM SULPHATE, HEPES PH 7.5	Resolution 1.40 Å R-free 0.220
2XLE Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124K variant with bound NO Deposited 2010-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PH7.5	Resolution 1.12 Å R-free 0.181
2XLH REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS Deposited 2010-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS-BUFFER PH 7.5	Resolution 1.14 Å R-free 0.161
2XLM Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous recombinant native with bound NO Deposited 2010-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO NITRIC OXIDE × 2 HEC HEME C × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PH 7.5	Resolution 1.19 Å R-free 0.200
2XLO Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124E variant with bound NO Deposited 2010-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PH 7.5	Resolution 1.24 Å R-free 0.200
2XLV Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124F variant with bound NO Deposited 2010-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 1.24 Å R-free 0.213
2XLW Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124Q variant with bound NO Deposited 2010-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–123（123 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 1.17 Å R-free 0.191
2XM0 Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124K variant Deposited 2010-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PH7.5	Resolution 1.25 Å R-free 0.222
2XM4 Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124E variant Deposited 2010-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；AMMONIUM SULPHATE, HEPES PH7.5, pH 7.4	Resolution 1.10 Å R-free 0.170
2YKZ RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT Deposited 2011-05-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5 .	Resolution 0.84 Å R-free 0.116
2YL0 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16A VARIANT AT 0.95 A RESOLUTION Deposited 2011-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 0.95 Å R-free 0.150
2YL1 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16A VARIANT AT 1.03 A RESOLUTION - Restraint refinement Deposited 2011-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 1.03 Å R-free 0.143
2YL3 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16G VARIANT AT 1.04 A RESOLUTION - RESTRAINT REFINED Deposited 2011-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CMO CARBON MONOXIDE × 2 HEC HEME C × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5.	Resolution 1.04 Å R-free 0.146
2YL7 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G VARIANT AT 0.9 A RESOLUTION - RESTRAINT REFINEMENT Deposited 2011-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 0.90 Å R-free 0.140
2YLD RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A Deposited 2011-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5 .	Resolution 1.25 Å R-free 0.190
2YLG CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND CARBON MONOOXIDE BOUND L16A VARIANT AT 1.05 A RESOLUTION Deposited 2011-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5.	Resolution 1.05 Å R-free 0.151
2YLI RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS IN ITS FERROUS FORM AT 1.45 A Deposited 2011-06-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 1.45 Å R-free 0.184
3ZQV RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: NON-RESTRAINED REFINEMENT Deposited 2011-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, PH 7.5	Resolution 0.84 Å
3ZQY CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16A VARIANT AT 1.03 A RESOLUTION- NON-RESTRAINT REFINEMENT Deposited 2011-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–127（126 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, PH 7.5.	Resolution 1.03 Å
3ZTM Cytochrome c prime from alcaligenes xylosoxidans: as isolated L16G variant at 0.9 A resolution: unrestraint refinement Deposited 2011-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, TRIS PH 7.5.	Resolution 0.90 Å
3ZTZ Cytochrome c prime from alcaligenes xylosoxidans: carbon monooxide bound L16G variant at 1.05 A resolution: unrestraint refinement Deposited 2011-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PH 7.5.	Resolution 1.05 Å
3ZWI RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A:UNRESTRAINT REFINEMENT Deposited 2011-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 CMO CARBON MONOXIDE × 2 SO4 SULFATE ION × 2 ASC ASCORBIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES BUFFER., pH 7.5	Resolution 1.25 Å R-free 0.187
4CDA Spectroscopically-validated structure of ferric cytochrome c prime from Alcaligenes xylosoxidans Deposited 2013-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES PH 7.5	Resolution 1.30 Å R-free 0.179
4CDV Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 100K Deposited 2013-11-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES PH 7.5	Resolution 1.17 Å R-free 0.160
4CDY Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 160K Deposited 2013-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES PH 7.5	Resolution 1.77 Å R-free 0.239
4CIP Spectroscopically-validated structure of ferrous cytochrome c prime from Alcaligenes xylosoxidans, reduced using ascorbate Deposited 2013-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES PH 7.5	Resolution 1.22 Å R-free 0.171
4CJG Spectroscopically validated structure of the 5 coordinate proximal NO adduct of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2013-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PG 7.5	Resolution 1.26 Å R-free 0.195
4CJO Spectroscopically-validated structure of ferrous cytochrome c prime from Alcaligenes xylosoxidans, reduced at 180K using X-rays Deposited 2013-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULPHATE, HEPES PH 7.5	Resolution 1.55 Å R-free 0.251
4D4N Nitrosyl complex of the D121A variant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2014-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES PH 7.5	Resolution 1.45 Å R-free 0.201
4D4X Nitrosyl complex of the D121I variant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2014-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES PH 7.5	Resolution 1.30 Å R-free 0.214
4WGY Crystal Structure of Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015 at pH 10.4 Deposited 2014-09-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.4；293 K；24 % PEG4000, 100 mM CAPS, 50 mM magnesium chloride	Resolution 1.48 Å R-free 0.173
4WGZ Crystal Structure of Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015 at pH 6.0 Deposited 2014-09-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 6；293 K；12 % PEG4000, 100 mM potassium phosphate, 1 mM sodium azide	Resolution 1.11 Å R-free 0.162
5AGF Nitrosyl complex of the D121Q variant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2015-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–127（126 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；AMMONIUM SULFATE, HEPES, pH 7.5	Resolution 1.09 Å R-free 0.185
5JLI Nitric oxide complex of the L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2016-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：L16A Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 4 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5	Resolution 1.55 Å R-free 0.214
5JP7 Ferrous Leu 16 Val mutant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2016-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–126（125 aa）	Mutation：L16V Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2 M Ammonium sulfate 0.1 M HEPES pH 7.5	Resolution 1.26 Å R-free 0.215
5JRA Nitric oxide complex of the L16V mutant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2016-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–126（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M Ammonium sulfate 0.1 M HEPES pH 7.5	Resolution 1.38 Å R-free 0.186
5JS5 Nitric oxide complex of the L16F mutant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2016-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 ASC ASCORBIC ACID × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M Ammonium sulfate 0.1M Hepes pH 7.5	Resolution 1.70 Å R-free 0.258
5JSL The L16F mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous form Deposited 2016-05-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–126（126 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5	Resolution 1.25 Å R-free 0.179
5JT4 L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state Deposited 2016-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 ASC ASCORBIC ACID × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M Ammonium sulfate 0.1 M HEPES pH 7.5	Resolution 1.25 Å R-free 0.191
5JUA Nitric oxide complex of the L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans Deposited 2016-05-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–126（126 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2 M Ammonium sulfate, 0.1M HEPES pH 7.5	Resolution 1.13 Å R-free 0.187
5JVE L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state Deposited 2016-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M Ammonium sulfate, 0.1 M HEPES pH 7.5	Resolution 1.12 Å R-free 0.181
5NC0 The 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide Deposited 2017-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–127（127 aa）	Mutation：L16G Non-standard monomer：Yes (specific site not provided by mmCIF)	HEC HEME C × 2 NO NITRIC OXIDE × 2 NO3 NITRATE ION × 2 NO2 NITRITE ION × 4 SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；AMMONIUM SULPHATE, TRIS PH 7.5	Resolution 0.91 Å R-free 0.132

50 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYCP_ALCXX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 1–126

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ngx
Deposition date deposition_date	2017-03-20
Structure title title	The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite
Keywords keywords	nitrite, cytochrome, homodimer, oxidoreductase, ferric, heme; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.25 Å
Radius of gyration Rg (electron density) rg_electron	15.35 Å
Forward intensity I(0) i0	3896690.00
Molecular weight molecular_weight	14032.0 kDa
Excluded volume excluded_volume	17522 Å³
Envelope volume envelope_volume	20292 Å³
Hydration-shell volume shell_volume	11722 Å³
Envelope diameter envelope_diameter	53.1 Å
Shell Rg shell_rg	20.31 Å
Envelope Rg envelope_rg	15.75 Å
Shape Rg shape_rg	15.35 Å
Total Rg total_rg	16.33 Å
Total atoms total_atoms	988
Residues n_residues	125
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	54.5 Å
Rg (real space) rg_real	16.28 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	3.8970e+06
I(0) uncertainty (real space) i0_real_error	4.8000e+04
Rg (reciprocal space) rg_reciprocal	16.28 Å
I(0) (reciprocal space) i0_reciprocal	3897000.0000
Solution quality estimate total_estimate	0.8630
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.8 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.318
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1032000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;Cytochrome c' ;
Molecular weight formula_weight	13446.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1310

QFAKPEDAVKYRQSAGTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRKK

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

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NITRITE ION
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	214

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5ngxa_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

CATH v4.4 (1 domains)

Domain ID domain_id	5ngxA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

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8. Citations (1)

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Unit-cell length a length_a	53.910 Å
Unit-cell length b length_b	53.910 Å
Unit-cell length c length_c	183.210 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.060 Å
Low-resolution limit resolution_low	45.240 Å
R factor r_factor	0.1787
R_work r_work	0.1776
R_free r_free	0.2001

fit	/app/data/saxs_computation/ng/5ngx/5ngx.fit
pddf	/app/data/pr_computation/ng/5ngx/5ngx.pr.out
profile	/app/data/saxs_computation/ng/5ngx/5ngx.dat