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Yorodumi- PDB-3v3y: Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v3y | ||||||
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Title | Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | ELECTRON TRANSPORT / Photosynthetic reaction center / Primary electron donor / membrane | ||||||
Function / homology | Function and homology information 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 | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gabdulkhakov, A.G. / Fufina, T.Y. / Vasilieva, L.G. / Shuvalov, V.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v3y.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v3y.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 3v3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/3v3y ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v3y | HTTPS FTP |
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-Related structure data
Related structure data | 3v3zC 1e6dS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | heterotrimer |
-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.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Plasmid: pREH-D2 L177 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y7 |
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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.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Plasmid: pREH-D2 L177 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 33885.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: pREH-D2 L177 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y9 |
-Non-polymers , 10 types, 117 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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