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- PDB-3prc: PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3prc | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED) | ||||||
![]() | (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: 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. #1: ![]() 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.D. / Michel, H. #2: ![]() Title: Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications Authors: Lancaster, C.R.D. #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 | ![]() | 273.6 KB | Display | ![]() |
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PDB format | ![]() | 224.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2prcSC 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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1 | ![]()
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2 |
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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 , 9 types, 449 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/BCB.gif)
![](data/chem/img/BPB.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/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-LDA / ![]() #9: Chemical | ChemComp-FE2 / | #10: Chemical | ChemComp-SO4 / ![]() #11: Chemical | ChemComp-MQ7 / | ![]() #12: Chemical | ChemComp-NS5 / | #13: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5 Å3/Da | ||||||||||||||||||
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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: Jul 1, 1993 / Details: FOCUSING MIRROR, TOROIDAL MIRROR | |||||||||
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→27.7 Å / Num. obs: 89029 / % possible obs: 79.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 6.9 | |||||||||
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.287 / % possible all: 60 | |||||||||
Reflection | *PLUS Num. obs: 87694 / Num. measured all: 233535 | |||||||||
Reflection shell | *PLUS % possible obs: 61.1 % |
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Processing
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Refinement | Method to determine structure![]() Starting model: PDB ENTRY 2PRC Resolution: 2.4→10 Å / Rfactor Rfree error: 0.0023 / Cross valid method: A POSTERIORI / Details: N(OBS)/N(PAR) = 2.07
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Displacement parameters | Biso mean: 28.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.207 / Rfactor obs: 0.168 |