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Yorodumi- PDB-1pcs: THE 2.15 A CRYSTAL STRUCTURE OF A TRIPLE MUTANT PLASTOCYANIN FROM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pcs | ||||||
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Title | THE 2.15 A CRYSTAL STRUCTURE OF A TRIPLE MUTANT PLASTOCYANIN FROM THE CYANOBACTERIUM SYNECHOCYSTIS SP. PCC 6803 | ||||||
Components | PLASTOCYANIN | ||||||
Keywords | ELECTRON TRANSPORT / PLASTOCYANIN | ||||||
Function / homology | Function and homology information plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Romero, A. / De La Cerda, B. / Varela, P.F. / Navarro, J.A. / Hervas, M. / De La Rosa, M.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The 2.15 A crystal structure of a triple mutant plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803. Authors: Romero, A. / De la Cerda, B. / Varela, P.F. / Navarro, J.A. / Hervas, M. / De la Rosa, M.A. #1: Journal: Biochemistry / Year: 1996 Title: Solution Structure of Reduced Plastocyanin from the Blue-Green Alga Anabaena Variabilis Authors: Badsberg, U. / Jorgensen, A.M. / Gesmar, H. / Led, J.J. / Hammerstad, J.M. / Jespersen, L.L. / Ulstrup, J. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Oxidized Poplar Plastocyanin at 1.6 A Resolution Authors: Guss, J.M. / 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 | 1pcs.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pcs.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pcs ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pcs | HTTPS FTP |
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-Related structure data
Related structure data | 1pcy S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10331.574 Da / Num. of mol.: 1 / Mutation: A42D, D47P, A63L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5A / References: UniProt: P21697 |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
Sequence details | WHEN SYNECHOCYSTIS PS IS ALIGNED WITH THE AMINO ACID SEQUENCE OF POPLAR PC, THE SEQUENCE OF ...WHEN SYNECHOCYS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 37 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PROTEIN WAS CRYSTALLIZED FROM 3.2M AMMONIUM SULFATE, 0.1M NA,K.PHOSPHATE, PH 6.0 WITH A PROTEIN CONCENTRATION OF 10 MG/ML | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20.3 Å / Num. obs: 4422 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 12.72 Å2 / Rsym value: 0.065 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 8.2 / Rsym value: 0.074 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 26699 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.074 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PCY 1pcy Resolution: 2.15→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 11.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 4070 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.174 |