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- PDB-2pcy: THE CRYSTAL STRUCTURE OF POPLAR APOPLASTOCYANIN AT 1.8-ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 2pcy
TitleTHE CRYSTAL STRUCTURE OF POPLAR APOPLASTOCYANIN AT 1.8-ANGSTROMS RESOLUTION. THE GEOMETRY OF THE COPPER-BINDING SITE IS CREATED BY THE POLYPEPTIDE
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT PROTEIN(CUPROPROTEIN)
Function / homology
Function and homology information


: / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding
Similarity search - Function
Plastocyanin / 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
Plastocyanin A, chloroplastic
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGarrett, T.P.J. / Guss, J.M. / Freeman, H.C.
Citation
Journal: J.Biol.Chem. / Year: 1984
Title: The crystal structure of poplar apoplastocyanin at 1.8-A resolution. The geometry of the copper-binding site is created by the polypeptide
Authors: Garrett, T.P. / Clingeleffer, D.J. / Guss, J.M. / Rogers, S.J. / Freeman, H.C.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Oxidized Poplar Plastocyanin at 1.6 Angstroms Resolution
Authors: Guss, J.M. / Freeman, H.C.
#2: Journal: Nature / Year: 1978
Title: X-Ray Crystal Structure Analysis of Plastocyanin at 2.7 Angstroms Resolution
Authors: Colman, P.M. / Freeman, H.C. / Guss, J.M. / Murata, M. / Norris, V.A. / Ramshaw, J.A.M. / Venkatappa, M.P.
History
DepositionNov 3, 1983Processing site: BNL
Revision 1.0Feb 2, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASTOCYANIN


Theoretical massNumber of molelcules
Total (without water)10,4941
Polymers10,4941
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.530, 46.800, 57.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 16 AND 36 ARE CIS-PROLINES.

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Components

#1: Protein PLASTOCYANIN


Mass: 10493.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus nigra (black poplar) / References: UniProt: P00299
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal grow
*PLUS
Method: other / Details: Chapman, G.V., (1977) J. Mol. Biol., 110, 187.

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. all: 7891 / Num. obs: 7103 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.029

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Processing

SoftwareName: RESTRAINED / Version: RECIPROCAL-SPACE LEAST-SQUARES REFINEMENT / Classification: refinement
RefinementResolution: 1.8→7 Å / Rfactor Rwork: 0.16 / σ(I): 1
Refinement stepCycle: LAST / Resolution: 1.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 0 42 780

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