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3l45

A Joint Neutron and X-ray structure of Oxidized Amicyanin

Dmax: 45.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Amicyanin

Paracoccus denitrificans

UniProt P22364

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 27–131 Fragment：UNP residues 27-131 CU COPPER (II) ION × 1 Experimental method not declared X-ray crystallization conditions：291 K；2.4M ammonium sulfate, 100mM citric acid pH5 and 3M sodium monobasic/potassium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 1.80 Å

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 3L45 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AAC AMICYANIN OXIDIZED, 1.31 ANGSTROMS Deposited 1995-09-07 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.31 Å
1AAJ CRYSTAL STRUCTURE ANALYSIS OF AMICYANIN AND APOAMICYANIN FROM PARACOCCUS DENITRIFICANS AT 2.0 ANGSTROMS AND 1.8 ANGSTROMS RESOLUTION Deposited 1992-04-09 Different construct Different ligand/ion Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1AAN CRYSTAL STRUCTURE ANALYSIS OF AMICYANIN AND APOAMICYANIN FROM PARACOCCUS DENITRIFICANS AT 2.0 ANGSTROMS AND 1.8 ANGSTROMS RESOLUTION Deposited 1992-04-09 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1BXA AMICYANIN REDUCED, PH 4.4, 1.3 ANGSTROMS Deposited 1998-10-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded CU1 COPPER (I) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.38；pH 4.38
Resolution 1.30 Å R-free 0.195
1MDA CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN Deposited 1992-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 29–131（103 aa）
Chain B 29–131（103 aa）
Not recorded CU COPPER (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1MG2 MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN Deposited 2002-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 27–131（105 aa）
Chain G 27–131（105 aa）
Not recorded PO4 PHOSPHATE ION × 4 CU COPPER (II) ION × 2 NA SODIUM ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.25 Å R-free 0.210
1MG2 MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN Deposited 2002-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 27–131（105 aa）
Chain O 27–131（105 aa）
Not recorded PO4 PHOSPHATE ION × 4 CU COPPER (II) ION × 2 NA SODIUM ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.25 Å R-free 0.210
1MG3 MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN Deposited 2002-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 27–131（105 aa）
Chain G 27–131（105 aa）
Not recorded PO4 PHOSPHATE ION × 4 CU COPPER (II) ION × 2 NA SODIUM ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.40 Å R-free 0.246
1MG3 MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN Deposited 2002-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 27–131（105 aa）
Chain O 27–131（105 aa）
Not recorded PO4 PHOSPHATE ION × 4 CU COPPER (II) ION × 2 NA SODIUM ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.40 Å R-free 0.246
1SF3 Structure of the reduced form of the P94A mutant of amicyanin Deposited 2004-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：P94A CU1 COPPER (I) ION × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5；293 K；3.6 M monobasic sodium phosphate, 0.4 M dibasic potassium phosphate, pH 5.0, EVAPORATION, temperature 293.0K
Resolution 1.05 Å R-free 0.147
1SF5 Structure of oxidized state of the P94A mutant of amicyanin Deposited 2004-02-19 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：P94A Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5；293 K；3.6 M monobasic sodium phosphate, 0.4 M dibasic potassium phosphate, pH 5.0, EVAPORATION, temperature 293.0K
Resolution 1.10 Å R-free 0.166
1SFD oxidized form of amicyanin mutant P94F Deposited 2004-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：P94F CU COPPER (II) ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；100 mM sodium citrate, 2.25 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 0.99 Å R-free 0.147
1SFD oxidized form of amicyanin mutant P94F Deposited 2004-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–131（105 aa）
Mutation：P94F CU COPPER (II) ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；100 mM sodium citrate, 2.25 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 0.99 Å R-free 0.147
1SFH Reduced state of amicyanin mutant P94F Deposited 2004-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：P94F CU1 COPPER (I) ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；80% 2.5 M monobasic sodium phosphate, 20% 2.5 M dibasic potassium phosphate, pH 5.5, EVAPORATION, temperature 293.0K
Resolution 1.05 Å R-free 0.153
1SFH Reduced state of amicyanin mutant P94F Deposited 2004-02-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–131（105 aa）
Mutation：P94F CU1 COPPER (I) ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；80% 2.5 M monobasic sodium phosphate, 20% 2.5 M dibasic potassium phosphate, pH 5.5, EVAPORATION, temperature 293.0K
Resolution 1.05 Å R-free 0.153
1T5K Crystal structure of amicyanin substituted with cobalt Deposited 2004-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded CO COBALT (II) ION × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；3.6 M monobasic sodium phosphate, 0.4 M dibasic potassium phosphate, pH 5.5, EVAPORATION, temperature 293.0K
Resolution 1.40 Å R-free 0.210
1T5K Crystal structure of amicyanin substituted with cobalt Deposited 2004-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–131（105 aa）
Not recorded CO COBALT (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；3.6 M monobasic sodium phosphate, 0.4 M dibasic potassium phosphate, pH 5.5, EVAPORATION, temperature 293.0K
Resolution 1.40 Å R-free 0.210
1T5K Crystal structure of amicyanin substituted with cobalt Deposited 2004-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 27–131（105 aa）
Not recorded CO COBALT (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；3.6 M monobasic sodium phosphate, 0.4 M dibasic potassium phosphate, pH 5.5, EVAPORATION, temperature 293.0K
Resolution 1.40 Å R-free 0.210
1T5K Crystal structure of amicyanin substituted with cobalt Deposited 2004-05-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 27–131（105 aa）
Not recorded CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；3.6 M monobasic sodium phosphate, 0.4 M dibasic potassium phosphate, pH 5.5, EVAPORATION, temperature 293.0K
Resolution 1.40 Å R-free 0.210
2GB2 The P52G mutant of amicyanin in the Cu(II) state. Deposited 2006-03-09 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：P52G CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 4.3；293 K；2.67 M sodium phosphate, 80:20 monobasic:dibasic, covered with mineral oil, pH 4.3, EVAPORATION, temperature 293K
Resolution 1.25 Å R-free 0.184
2GBA Reduced Cu(I) form at pH 4 of P52G mutant of amicyanin Deposited 2006-03-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：P52G CU1 COPPER (I) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 4.3；293 K；3.0 M sodium phosphate 90:10 monobasic:dibasic covered drop in mineral oil, pH 4.3, EVAPORATION, temperature 293K
Resolution 0.92 Å R-free 0.147
2GC4 Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M Sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.197
2GC4 Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M Sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.197
2GC4 Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M Sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.197
2GC4 Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M Sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.197
2GC7 Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 27–131（105 aa）
Not recorded NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.198
2GC7 Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 27–131（105 aa）
Not recorded NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.198
2GC7 Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 27–131（105 aa）
Not recorded NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.198
2GC7 Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans. Deposited 2006-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 27–131（105 aa）
Not recorded NA SODIUM ION × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；2.3-2.6M sodium/potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.198
2IDQ Structure of M98A mutant of amicyanin, Cu(II) Deposited 2006-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M98A CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；10 mg/ml amicyanin in 3.0 M phosphate, pH 5.5, EVAPORATION, temperature 293K
Resolution 0.90 Å R-free 0.130
2IDS Structure of M98A mutant of amicyanin, Cu(I) Deposited 2006-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M98A CU1 COPPER (I) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；3.0 M phosphate, pH 5.5, EVAPORATION, temperature 293K
Resolution 1.00 Å R-free 0.170
2IDT Structure of M98Q mutant of amicyanin, Cu(II) Deposited 2006-09-15 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M98Q Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；2.6 M phosphate, pH 5.5, EVAPORATION, temperature 293K
Resolution 1.00 Å R-free 0.158
2IDU Structure of M98Q mutant of amicyanin, Cu(I) Deposited 2006-09-15 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M98Q Non-standard monomer：Yes (specific site not provided by mmCIF) CU1 COPPER (I) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；2.6 M phosphate, pH 5.5, EVAPORATION, temperature 293K
Resolution 0.95 Å R-free 0.162
2J55 X-ray reduced Paraccocus denitrificans methylamine dehydrogenase O- quinone in complex with amicyanin. Deposited 2006-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 27–131（105 aa）
Chain B 27–131（105 aa）
Not recorded CU COPPER (II) ION × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.15 Å R-free 0.245
2J56 X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin. Deposited 2006-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 27–131（105 aa）
Chain B 27–131（105 aa）
Not recorded CU COPPER (II) ION × 2 GOL GLYCEROL × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；pH 9.00
Resolution 2.10 Å R-free 0.207
2J57 X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin. Deposited 2006-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 27–131（105 aa）
Chain B 27–131（105 aa）
Not recorded CU COPPER (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.25 Å R-free 0.241
2J57 X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin. Deposited 2006-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 27–131（105 aa）
Chain D 27–131（105 aa）
Not recorded CU COPPER (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.25 Å R-free 0.241
2MTA CRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE, AMICYANIN AND A C-TYPE CYTOCHROME Deposited 1993-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 27–131（105 aa）
Not recorded PO4 PHOSPHATE ION × 2 CU COPPER (II) ION × 2 HEC HEME C × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
2OV0 Structure of the blue copper protein Amicyanin to 0.75 A resolution Deposited 2007-02-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；3 M sodium phosphate, pH 5.5, EVAPORATION, temperature 293K
Resolution 0.75 Å R-free 0.142
2QDV Structure of the Cu(II) form of the M51A mutant of amicyanin Deposited 2007-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M51A Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；2.5-3 M phosphate, 10 mg/ml amicyanin, pH 5.5, EVAPORATION, temperature 293K
Resolution 0.89 Å R-free 0.135
2QDW Structure of Cu(I) form of the M51A mutant of amicyanin Deposited 2007-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M51A Non-standard monomer：Yes (specific site not provided by mmCIF) CU1 COPPER (I) ION × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；2.5-3.0 M phosphate 10 mg/ml amicyanin, pH 5.5, EVAPORATION, temperature 293K
Resolution 0.92 Å R-free 0.147
2RAC AMICYANIN REDUCED, PH 7.7, 1.3 ANGSTROMS Deposited 1998-10-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Not recorded CU1 COPPER (I) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；pH 7.70
Resolution 1.30 Å R-free 0.210
3IE9 Structure of oxidized M98L mutant of amicyanin Deposited 2009-07-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa） Fragment：residues 27-131
Mutation：M98L PO4 PHOSPHATE ION × 1 CU COPPER (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.10 Å R-free 0.214
3IE9 Structure of oxidized M98L mutant of amicyanin Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 27–131（105 aa） Fragment：residues 27-131
Mutation：M98L PO4 PHOSPHATE ION × 6 CU COPPER (II) ION × 6 ZN ZINC ION × 6 CL CHLORIDE ION × 6 ACT ACETATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.10 Å R-free 0.214
3IE9 Structure of oxidized M98L mutant of amicyanin Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 27–131（105 aa） Fragment：residues 27-131
Mutation：M98L PO4 PHOSPHATE ION × 3 CU COPPER (II) ION × 3 ZN ZINC ION × 3 CL CHLORIDE ION × 3 ACT ACETATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.10 Å R-free 0.214
3IEA Structure of reduced M98L mutant of amicyanin Deposited 2009-07-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa） Fragment：residues 27-131
Mutation：M124L PO4 PHOSPHATE ION × 1 CU COPPER (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.200
3IEA Structure of reduced M98L mutant of amicyanin Deposited 2009-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 27–131（105 aa） Fragment：residues 27-131
Mutation：M124L PO4 PHOSPHATE ION × 6 CU COPPER (II) ION × 6 ZN ZINC ION × 6 CL CHLORIDE ION × 6 ACT ACETATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.200
3PLY Structure of Oxidized P96G Mutant of Amicyanin Deposited 2010-11-15 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa） Fragment：UNP residues 27-131
Mutation：P96G CU COPPER (II) ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.8M sodium/potassium phosphate pH 7.5, 40mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.291
3PLY Structure of Oxidized P96G Mutant of Amicyanin Deposited 2010-11-15 Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–131（105 aa） Fragment：UNP residues 27-131
Mutation：P96G CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.8M sodium/potassium phosphate pH 7.5, 40mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.291
3PLY Structure of Oxidized P96G Mutant of Amicyanin Deposited 2010-11-15 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 27–131（105 aa） Fragment：UNP residues 27-131
Mutation：P96G CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.8M sodium/potassium phosphate pH 7.5, 40mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.291
3PLY Structure of Oxidized P96G Mutant of Amicyanin Deposited 2010-11-15 Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 27–131（105 aa） Fragment：UNP residues 27-131
Mutation：P96G CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.8M sodium/potassium phosphate pH 7.5, 40mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.291
3RYM Structure of Oxidized M98K mutant of Amicyanin Deposited 2011-05-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa）
Mutation：M98K ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.01M zinc sulphate heptahydrate, 0.1M MES pH 6.5, 25% w/v PEG monomethylether 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.70 Å R-free 0.215
3RYM Structure of Oxidized M98K mutant of Amicyanin Deposited 2011-05-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–131（105 aa）
Mutation：M98K ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.01M zinc sulphate heptahydrate, 0.1M MES pH 6.5, 25% w/v PEG monomethylether 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.70 Å R-free 0.215
3RYM Structure of Oxidized M98K mutant of Amicyanin Deposited 2011-05-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 27–131（105 aa）
Mutation：M98K ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.01M zinc sulphate heptahydrate, 0.1M MES pH 6.5, 25% w/v PEG monomethylether 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.70 Å R-free 0.215
3RYM Structure of Oxidized M98K mutant of Amicyanin Deposited 2011-05-11 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 27–131（105 aa）
Mutation：M98K ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.01M zinc sulphate heptahydrate, 0.1M MES pH 6.5, 25% w/v PEG monomethylether 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.70 Å R-free 0.215
4P5R Structure of oxidized W45Y mutant of amicyanin Deposited 2014-03-19 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa） Fragment：UNP residues 27-131
Mutation：W45Y CU COPPER (II) ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Initial crystals were obtained from Hampton research ammonium sulfate screen (HR2-211). Bigger crystals grown by macro-seeding using 3.2M Na/K phosphate solution.
Resolution 1.09 Å R-free 0.153
4P5S Structure of reduced W45Y mutant of amicyanin Deposited 2014-03-19 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–131（105 aa） Fragment：UNP residues 27-131
Mutation：W45Y CU1 COPPER (I) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Initial crystals were obtained from Hampton research ammonium sulfate screen (HR2-211). Bigger crystals grown by macro-seeding using 3.2M Na/K phosphate solution.
Resolution 1.02 Å R-free 0.150

34 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMCY_PARDE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–105； UniProt 27–131

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 3l45

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3l45
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3l45
Deposition date deposition_date2009-12-18
Structure title titleA Joint Neutron and X-ray structure of Oxidized Amicyanin
Keywords keywordsType-I Blue Copper Protein, Beta Sandwich, Electron Transport, Metal-binding; ELECTRON TRANSPORT
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.52 Å
Radius of gyration Rg (electron density) rg_electron12.94 Å
Forward intensity I(0) i03410320.00
Molecular weight molecular_weight13686.0 kDa
Excluded volume excluded_volume17181 ų
Envelope volume envelope_volume19860 ų
Hydration-shell volume shell_volume12392 ų
Envelope diameter envelope_diameter43.5 Å
Shell Rg shell_rg19.45 Å
Envelope Rg envelope_rg13.69 Å
Shape Rg shape_rg13.27 Å
Total Rg total_rg13.46 Å
Total atoms total_atoms1878
Residues n_residues105
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 dmax45.0 Å
Rg (real space) rg_real14.42 Å
Rg uncertainty (real space) rg_real_error0.18 Å
I(0) (real space) i0_real3.4100e+06
I(0) uncertainty (real space) i0_real_error3.5010e+04
Rg (reciprocal space) rg_reciprocal14.43 Å
I(0) (reciprocal space) i0_reciprocal3410000.0000
Solution quality estimate total_estimate0.8970
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness0.096
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha913000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3l45a_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (1 domains)

Domain ID domain_id3l45A00
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 (2)

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9. Files and Curves (10)