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- PDB-6prc: PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (DG-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6prc | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (DG-420314 (TRIAZINE) COMPLEX) | ||||||
![]() | (PHOTOSYNTHETIC REACTION ...) x 4 | ||||||
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Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lancaster, C.R.D. / Michel, H. | ||||||
![]() | ![]() Title: Refined crystal structures of reaction centres from Rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid. Authors: Lancaster, C.R. / Michel, H. #1: ![]() Title: Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications Authors: Lancaster, C.R.D. #2: ![]() Title: The Coupling of Light-Induced Electron Transfer and Proton Uptake as Derived from Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb Authors: Lancaster, C.R. / Michel, H. #3: ![]() 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. #4: ![]() Title: The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis Authors: Deisenhofer, J. / Michel, H. #5: ![]() 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. #6: ![]() Title: X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A 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. #7: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.9 KB | Display | ![]() |
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PDB format | ![]() | 223.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5prcC ![]() 7prcC ![]() 2prcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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 natural source / Source: (natural) ![]() ![]() |
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#2: Protein | ![]() Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | ![]() Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | ![]() Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 10 types, 361 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/CEB.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.gif)
![](data/chem/img/CEB.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MQ7.gif)
![](data/chem/img/NS5.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HEM / ![]() #6: Chemical | ChemComp-BCB / ![]() #7: Chemical | ![]() #8: Chemical | ChemComp-CEB / | #9: Chemical | ChemComp-LDA / ![]() #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-SO4 / ![]() #12: Chemical | ChemComp-MQ7 / | ![]() #13: Chemical | ChemComp-NS5 / | #14: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 70 % | ||||||||||||||||||
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Crystal grow![]() | pH: 6 / Details: pH 6.0 | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 263 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1993 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→30 Å / Num. obs: 102956 / % possible obs: 81 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.247 / % possible all: 51.8 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 102117 / % possible obs: 81.4 % / Num. measured all: 256827 |
Reflection shell | *PLUS % possible obs: 56.6 % |
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Processing
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Refinement | Method to determine structure![]() Starting model: PDB ENTRY 2PRC Resolution: 2.3→10 Å / Rfactor Rfree error: 0.0022 / Cross valid method: A POSTERIORI / σ(F): 1.5 / Details: N(OBS)/N(PAR) = 2.43
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Displacement parameters | Biso mean: 32.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 10498 / Rfactor Rfree![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.287 |