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Yorodumi- PDB-4n7l: Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n7l | ||||||
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Title | Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter sphaeroides | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | PHOTOSYNTHESIS | ||||||
Function / homology | Function and homology information plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å | ||||||
Authors | Hardjasa, A. / Murphy, M.E.P. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Structural and kinetic properties of Rhodobacter sphaeroides photosynthetic reaction centers containing exclusively Zn-coordinated bacteriochlorophyll as bacteriochlorin cofactors. Authors: Saer, R.G. / Pan, J. / Hardjasa, A. / Lin, S. / Rosell, F. / Mauk, A.G. / Woodbury, N.W. / Murphy, M.E. / Beatty, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n7l.cif.gz | 220.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n7l.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 4n7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/4n7l ftp://data.pdbj.org/pub/pdb/validation_reports/n7/4n7l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 26122.035 Da / Num. of mol.: 1 / Mutation: L214H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: puhA, puhApufML / Plasmid: pRS1 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y7, UniProt: Q3J170*PLUS |
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#2: Protein | Mass: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: pufL, puhApufML / Plasmid: pRS1 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y8, UniProt: Q3J1A5*PLUS |
#3: Protein | Mass: 34028.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: pufM, puhApufML / Plasmid: pRS1 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y9, UniProt: Q3J1A6*PLUS |
-Non-polymers , 12 types, 427 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-GGD / | #6: Chemical | ChemComp-LDA / #7: Chemical | #8: Chemical | ChemComp-2GO / [ #9: Chemical | ChemComp-PO4 / | #10: Chemical | #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-SPO / | #13: Chemical | ChemComp-CDL / | #14: Chemical | ChemComp-PC1 / | #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 | Density Matthews: 5.66 Å3/Da / Density % sol: 78.26 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→120.888 Å / Num. obs: 42741 / % possible obs: 87.4 % / Redundancy: 7 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 12.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.85→50.57 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.1962 / WRfactor Rwork: 0.1515 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8782 / SU B: 8.92 / SU ML: 0.171 / SU R Cruickshank DPI: 0.4516 / SU Rfree: 0.2863 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 197.48 Å2 / Biso mean: 54.9718 Å2 / Biso min: 11.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→50.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Total num. of bins used: 20
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