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Yorodumi- PDB-3g7f: Crystal structure of Blastochloris viridis heterodimer mutant rea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g7f | ||||||
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Title | Crystal structure of Blastochloris viridis heterodimer mutant reaction center | ||||||
Components | (Photosynthetic reaction center ...) x 4 | ||||||
Keywords | PHOTOSYNTHESIS / Heterodimer mutant / Blastochloris viridis / photosynthetic reaction center / membrane protein structure / microfluidics / plugs / Cell membrane / Electron transport / Heme / Iron / Lipoprotein / Membrane / Metal-binding / Reaction center / Transport / Bacteriochlorophyll / Chlorophyll / Chromophore / Formylation / Transmembrane / Magnesium | ||||||
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 / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Blastochloris viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ponomarenko, N.S. / Li, L. / Tereshko, V. / Ismagilov, R.F. / Norris Jr., J.R. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center Authors: Ponomarenko, N.S. / Li, L. / Marino, A.R. / Tereshko, V. / Ostafin, A. / Popova, J.A. / Bylina, E.J. / Ismagilov, R.F. / Norris, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g7f.cif.gz | 292.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g7f.ent.gz | 230.6 KB | Display | PDB format |
PDBx/mmJSON format | 3g7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g7f_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 3g7f_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 3g7f_validation.xml.gz | 60 KB | Display | |
Data in CIF | 3g7f_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g7f ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g7f | HTTPS FTP |
-Related structure data
Related structure data | 2i5nS S: Starting model for refinement |
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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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-Components
-Photosynthetic reaction center ... , 4 types, 4 molecules CHLM
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: membrane / References: UniProt: P07173 |
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#2: Protein | Mass: 28527.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: membrane / References: UniProt: P06008 |
#3: Protein | Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: membrane / References: UniProt: P06009 |
#4: Protein | Mass: 35907.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: membrane / References: UniProt: P06010 |
-Non-polymers , 11 types, 773 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-HTO / #8: Chemical | ChemComp-LDA / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-FE2 / | #13: Chemical | ChemComp-MQ9 / | #14: Chemical | ChemComp-NS5 / | #15: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6 Details: Plug-based microfluidics, Precipitant was mixed with buffer and RC sample in a microfluidic chip. The final precipitant concentration was ~1.7 M ammonium sulfate, 0.1% LDAO,30 mM NaH2PO4- ...Details: Plug-based microfluidics, Precipitant was mixed with buffer and RC sample in a microfluidic chip. The final precipitant concentration was ~1.7 M ammonium sulfate, 0.1% LDAO,30 mM NaH2PO4-Na2HPO4, pH 6.0, 3% 1,2,3-heptanetriol, 1.9% triethylammonium phosphate. RC concentration was ~ 9.4 mg/mL, Microbatch, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 95377 / Redundancy: 7.1 % / Rmerge(I) obs: 0.137 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.709 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2i5n Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.165 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.995 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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