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Yorodumi- PDB-1prc: CRYSTALLOGRAPHIC REFINEMENT AT 2.3 ANGSTROMS RESOLUTION AND REFIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1prc | |||||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT AT 2.3 ANGSTROMS RESOLUTION AND REFINED MODEL OF THE PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS | |||||||||
Components | (PHOTOSYNTHETIC REACTION ...) x 4 | |||||||||
Keywords | PHOTOSYNTHETIC REACTION CENTER | |||||||||
Function / homology | Function and homology information plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Blastochloris viridis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | |||||||||
Authors | Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. Authors: Deisenhofer, J. / Epp, O. / Sinning, I. / Michel, H. #1: Journal: Science / Year: 1989 Title: The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis Authors: Deisenhofer, J. / Michel, H. #2: Journal: Nature / Year: 1985 Title: Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H. #3: Journal: J.Mol.Biol. / Year: 1984 Title: X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 Angstroms Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H. #4: Journal: J.Mol.Biol. / Year: 1982 Title: Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis Authors: Michel, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1prc.cif.gz | 266 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1prc.ent.gz | 223.8 KB | Display | PDB format |
PDBx/mmJSON format | 1prc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/1prc ftp://data.pdbj.org/pub/pdb/validation_reports/pr/1prc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO C 6, PRO C 153, PRO C 330, PRO M 48, PRO H 42, AND PRO H 79 ARE CIS PROLINES. 2: SEE REMARK 4. | ||||||||
Components on special symmetry positions |
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-Components
-PHOTOSYNTHETIC REACTION ... , 4 types, 4 molecules CLMH
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastochloris viridis (bacteria) / References: UniProt: P07173 |
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#2: Protein | Mass: 30469.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastochloris viridis (bacteria) / References: UniProt: P06009 |
#3: Protein | Mass: 35932.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastochloris viridis (bacteria) / References: UniProt: P06010 |
#4: Protein | Mass: 28557.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastochloris viridis (bacteria) / References: UniProt: P06008 |
-Non-polymers , 10 types, 224 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-BCB / #7: Chemical | #8: Chemical | ChemComp-UQ1 / | #9: Chemical | ChemComp-FE / | #10: Chemical | ChemComp-SO4 / #11: Chemical | ChemComp-MQ7 / | #12: Chemical | ChemComp-NS1 / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.36 Å3/Da / Density % sol: 77.04 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion / Details: Michel, H., (1982) J.Mol.Biol., 158, 567. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 95762 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 49.2 % |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.3→19.99 Å /
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.99 Å
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Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 22.5 Å2 |