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- PDB-5pcy: CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN A... -

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Basic information

Entry
Database: PDB / ID: 5pcy
TitleCRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES
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
COPPER (II) ION / Plastocyanin A, chloroplastic
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGuss, J.M. / Freeman, H.C.
Citation
Journal: J.Mol.Biol. / Year: 1986
Title: Crystal structure analyses of reduced (CuI) poplar plastocyanin at six pH values.
Authors: Guss, J.M. / Harrowell, P.R. / Murata, M. / Norris, V.A. / Freeman, H.C.
#1: Journal: J.Biol.Chem. / Year: 1986
Title: The Crystal Structure of Mercury-Substituted Poplar Plastocyanin at 1.9-Angstroms Resolution
Authors: Church, W.B. / Guss, J.M. / Potter, J.J. / Freeman, H.C.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: The Crystal Structure of Poplar Apoplastocyanin at 1.8-Angstroms Resolution. The Geometry of the Copper-Binding Site is Created by the Polypeptide
Authors: Garrett, T.P.J. / Clingeleffer, D.J. / Guss, J.M. / Rogers, S.J. / Freeman, H.C.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Oxidized Poplar Plastocyanin at 1.6 Angstroms Resolution
Authors: Guss, J.M. / Freeman, H.C.
#4: 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
DepositionSep 2, 1986Processing site: BNL
Revision 1.0Jan 15, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5572
Polymers10,4941
Non-polymers641
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.580, 46.560, 58.540
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. / 2: SEE REMARK 4.

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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: 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.: 44 / 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: 1.92 Å3/Da / Density % sol: 35.93 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion / Details: Chapman, G.V. (1977). J. Mol. Biol., 110, 187.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
20.1 Msodium phosphate1reservoir
32.6 Mammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 7 Å / Num. obs: 6971 / Num. measured all: 9478 / Rmerge(I) obs: 0.078

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.16 / Highest resolution: 1.8 Å
Details: THE SHORT CONTACT BETWEEN CE1 HIS 87 AND O PRO 36 (3.4 ANGSTROMS AT PH 7.8, 3.3 ANGSTROMS AT PH 7.0) IS REPLACED BY A WEAK HYDROGEN BOND (3.1 ANGSTROMS) BETWEEN NE2 HIS 87 AND O PRO 36 AFTER ...Details: THE SHORT CONTACT BETWEEN CE1 HIS 87 AND O PRO 36 (3.4 ANGSTROMS AT PH 7.8, 3.3 ANGSTROMS AT PH 7.0) IS REPLACED BY A WEAK HYDROGEN BOND (3.1 ANGSTROMS) BETWEEN NE2 HIS 87 AND O PRO 36 AFTER ROTATION OF THE HIS 87 SIDE CHAIN AT PH 3.8 (SEE *JRNL* REFERENCE ABOVE).
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 1 44 783
Refinement
*PLUS
Lowest resolution: 7 Å / Num. reflection obs: 6900 / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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