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Yorodumi- PDB-3t6e: Crystal Structure of the Reaction Centre from Blastochloris virid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t6e | ||||||
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Title | Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-94 | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Pigment-protein complex / Electron transfer / Photosynthesis / Photosynthetic reaction center / Photosynthetic membranes / Evolution / Genetic drift | ||||||
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: 1.92 Å | ||||||
Authors | Roszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J. | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory. Authors: Roszak, A.W. / Moulisova, V. / Reksodipuro, A.D. / Gardiner, A.T. / Fujii, R. / Hashimoto, H. / Isaacs, N.W. / Cogdell, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t6e.cif.gz | 621.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t6e.ent.gz | 507 KB | Display | PDB format |
PDBx/mmJSON format | 3t6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t6e_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 3t6e_full_validation.pdf.gz | 5.5 MB | Display | |
Data in XML | 3t6e_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 3t6e_validation.cif.gz | 103.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t6e ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t6e | HTTPS FTP |
-Related structure data
Related structure data | 3t6dSC 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: substrain-94 is identical at the amino acid level with the original strain DSM 133 Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173 |
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-Reaction center protein ... , 3 types, 3 molecules HLM
#2: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: substrain-94 is identical at the amino acid level with the original strain DSM 133 Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008 |
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#3: Protein | Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: substrain-94 is identical at the amino acid level with the original strain DSM 133 Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009 |
#4: Protein | Mass: 35948.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: substrain-94 is identical at the amino acid level with the original strain DSM 133 Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010 |
-Non-polymers , 13 types, 1084 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-LDA / #7: Chemical | ChemComp-DGA / #8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-HTO / #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-BCB / #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-MQ9 / | #15: Chemical | ChemComp-FE2 / | #16: Chemical | ChemComp-NS5 / | #17: 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: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein in 20 mM sodium phosphate buffer and 0.1% lauryldimethylamine N,N-oxide (LDAO) detergent, precipitant 1.5 M ammonium sulfate, amphiphile 3% heptanetriol, reservoir solution 2.2-2.4 M ...Details: Protein in 20 mM sodium phosphate buffer and 0.1% lauryldimethylamine N,N-oxide (LDAO) detergent, precipitant 1.5 M ammonium sulfate, amphiphile 3% heptanetriol, reservoir solution 2.2-2.4 M ammonium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9194 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010 / Details: Mirrors |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9194 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→43.46 Å / Num. all: 212134 / Num. obs: 212134 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.35 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.119 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 18.87 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.6 / Num. unique all: 20895 / Rsym value: 0.843 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3T6D Resolution: 1.92→43.46 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.678 / SU ML: 0.059 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→43.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.595 Å / Origin y: -49.212 Å / Origin z: 10.558 Å
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Refinement TLS group |
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