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Yorodumi- PDB-6pcy: CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN A... -
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-Basic information
Entry | Database: PDB / ID: 6pcy | ||||||
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Title | CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES | ||||||
Components | PLASTOCYANIN | ||||||
Keywords | ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN) | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Populus nigra (black poplar) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Guss, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pcy.cif.gz | 31 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pcy.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 6pcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/6pcy ftp://data.pdbj.org/pub/pdb/validation_reports/pc/6pcy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 16 AND 36 ARE CIS-PROLINES. / 2: SEE REMARK 5. |
-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
Compound details | THE SIDE CHAIN OF ASN 99 IS PROBABLY DISORDERED. THE ORIENTATION IN THE DEPOSITED COORDINATES IS ...THE SIDE CHAIN OF ASN 99 IS PROBABLY DISORDERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.8 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion / Details: Chapman, G.V. (1977). J. Mol. Biol., 110, 187. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 7 Å / Num. obs: 5810 / Num. measured all: 7225 / Rmerge(I) obs: 0.045 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.152 / Highest resolution: 1.9 Å Details: IN THIS STRUCTURE ONE OR MORE SIDE CHAIN ATOMS IN A NUMBER OF RESIDUES HAVE HIGH TEMPERATURE FACTORS AND ARE LOCATED IN EITHER WEAK OR INSIGNIFICANT ELECTRON DENSITY IN REMOVED MAPS (SEE ...Details: IN THIS STRUCTURE ONE OR MORE SIDE CHAIN ATOMS IN A NUMBER OF RESIDUES HAVE HIGH TEMPERATURE FACTORS AND ARE LOCATED IN EITHER WEAK OR INSIGNIFICANT ELECTRON DENSITY IN REMOVED MAPS (SEE *JRNL* REFERENCE ABOVE). THE DEPOSITED COORDINATES MAY THEREFORE REPRESENT ONE OF A NUMBER OF DISORDERED POSITIONS OR BE INCORRECTLY LOCATED. THE RESIDUES INVOLVED ARE LYS 26, LYS 30, GLU 43, SER 45, LYS 54, GLU 59, GLU 60, ASP 61, ASN 64, LYS 66, GLU 71, LYS 95, AND ASN 99. INTRA- AND INTERMOLECULAR CONTACTS AND COMPARISONS INVOLVING THOSE ATOMS SHOULD BE TREATED WITH CAUTION. 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 step | Cycle: LAST / Highest resolution: 1.9 Å
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Refinement | *PLUS Lowest resolution: 7 Å / Num. reflection obs: 5721 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |