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- PDB-3v3y: Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v3y | ||||||
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Title | Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | ELECTRON TRANSPORT / Photosynthetic reaction center / Primary electron donor / membrane | ||||||
Function / homology | ![]() plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gabdulkhakov, A.G. / Fufina, T.Y. / Vasilieva, L.G. / Shuvalov, V.A. | ||||||
![]() | ![]() Title: The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls. Authors: Vasilieva, L.G. / Fufina, T.Y. / Gabdulkhakov, A.G. / Leonova, M.M. / Khatypov, R.A. / Shuvalov, V.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.6 KB | Display | ![]() |
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PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v3zC ![]() 1e6dS 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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Details | heterotrimer |
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Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 26170.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 31360.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 33885.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 10 types, 117 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/DIO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-LDA / #5: Chemical | ChemComp-BCL / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-FE / | #10: Chemical | ChemComp-SPN / | #11: Chemical | #12: Chemical | ChemComp-CL / | #13: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE DISCREPANC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.72 Å3/Da / Density % sol: 78.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 3.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Nov 11, 2011 |
Radiation | Monochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→26.6 Å / Num. all: 52181 / Num. obs: 51787 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 6.11 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1E6D Resolution: 2.8→19.941 Å / SU ML: 0.9 / σ(F): 0 / Phase error: 28.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.091 Å2 / ksol: 0.274 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.941 Å
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Refine LS restraints |
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LS refinement shell |
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