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- PDB-1aac: AMICYANIN OXIDIZED, 1.31 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1aac
TitleAMICYANIN OXIDIZED, 1.31 ANGSTROMS
ComponentsAMICYANIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.31 Å
AuthorsCunane, L.M. / Chen, Z.-W. / Durley, R.C.E. / Mathews, F.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-ray structure of the cupredoxin amicyanin, from Paracoccus denitrificans, refined at 1.31 A resolution.
Authors: Cunane, L.M. / Chen, Z.W. / Durley, R.C. / Mathews, F.S.
#1: Journal: Protein Sci. / Year: 1993
Title: Crystal Structure Analysis of Amicyanin and Apoamicyanin from Paracoccus Denitrificans at 2.0 Angstroms and 1.8 Angstroms Resolution
Authors: Durley, R. / Chen, L. / Lim, L.W. / Mathews, F.S. / Davidson, V.L.
History
DepositionSep 7, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5051
Non-polymers641
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.950, 56.540, 27.550
Angle α, β, γ (deg.)90.00, 96.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AMICYANIN


Mass: 11505.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / Strain: NCIB 8944 / References: UniProt: P22364
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 Mphosphate1reservoir
2ammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 20, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.31→20.16 Å / Num. obs: 21219 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.0499
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 199399

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
SDMSdata reduction
X-PLOR2.1phasing
RefinementResolution: 1.31→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.155 --
obs0.155 21098 99 %
Displacement parametersBiso mean: 9.95 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.31→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 1 158 1014
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.84
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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