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Yorodumi- PDB-1pnd: ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pnd | ||||||
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Title | ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K | ||||||
Components | PLASTOCYANIN | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | Populus nigra (black poplar) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Fields, B.A. / Guss, J.M. / Freeman, H.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K. Authors: Fields, B.A. / Bartsch, H.H. / Bartunik, H.D. / Cordes, F. / Guss, J.M. / Freeman, H.C. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: Accuracy and Precision in Protein Structure Analysis: Restrained Least-Squares Refinement of the Structure of Poplar Plastocyanin at 1.33 Angstroms Resolution Authors: Guss, J.M. / Bartunik, H.D. / Freeman, H.C. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Oxidised Poplar Plastocyanin at 1.6 Angstroms Resolution Authors: Guss, J.M. / Freeman, H.C. #3: 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. / Freeman, H.C. #4: Journal: J.Mol.Biol. / Year: 1977 Title: Preliminary Crystallographic Data for a Copper Containing Protein, Plastocyanin Authors: Chapman, G.V. / Colman, P.M. / Freeman, H.C. / Guss, J.M. / Murata, M. / Norris, V.A. / Ramashaw, J.A.M. / Venkatappa, M.P. / Freeman, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pnd.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pnd.ent.gz | 22.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pnd_validation.pdf.gz | 357.6 KB | Display | wwPDB validaton report |
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Full document | 1pnd_full_validation.pdf.gz | 357.8 KB | Display | |
Data in XML | 1pnd_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1pnd_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/1pnd ftp://data.pdbj.org/pub/pdb/validation_reports/pn/1pnd | HTTPS FTP |
-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: CIS PROLINE - PRO 16 / 2: CIS PROLINE - PRO 36 3: THE LIGANDS OF THE CU ATOM ARE ND1 HIS 37, SG CYS 84, ND1 HIS 87, AND SD MET 92. |
-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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.48 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusionDetails: taken from Chapman, G.V. et al (1977). J. Mol. Biol., 110, 187-189. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 |
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Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 1.6→6 Å Details: THE STRUCTURE WAS REFINED INDEPENDENTLY IN SYDNEY USING PROLSQ AND IN HAMBURG USING EREF. THE STRUCTURES WERE COMPARED ONLY AFTER THE REFINEMENTS WERE COMPLETE.
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Refinement step | Cycle: LAST / Resolution: 1.6→6 Å
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Refine LS restraints |
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Software | *PLUS Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 6 Å / Num. reflection obs: 7393 / Rfactor obs: 0.135 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11 Å2 |