+Open data
-Basic information
Entry | Database: PDB / ID: 4in7 | ||||||
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Title | (M)L214N mutant of the Rhodobacter sphaeroides Reaction Center | ||||||
Components | (Reaction center protein ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Electron Transfer / Chromatophore | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Saer, R.G. / Hardjasa, A. / Murphy, M.E.P. / Beatty, J.T. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Role of Rhodobacter sphaeroides photosynthetic reaction center residue M214 in the composition, absorbance properties, and conformations of H(A) and B(A) cofactors. Authors: Saer, R.G. / Hardjasa, A. / Rosell, F.I. / Mauk, A.G. / 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 | 4in7.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4in7.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 4in7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4in7_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 4in7_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 4in7_validation.xml.gz | 43 KB | Display | |
Data in CIF | 4in7_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4in7 ftp://data.pdbj.org/pub/pdb/validation_reports/in/4in7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is dimeric and surrounded by PufX and LH1 complexes. |
-Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 28895.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: puhA / Plasmid: pRS1::(M)L214G / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y7 |
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#2: Protein | Mass: 31477.584 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 / Plasmid: pRS1::(M)L214G / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 34416.578 Da / Num. of mol.: 1 / Mutation: L214N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: pufM / Plasmid: pRS1::(M)L214G / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y9 |
-Non-polymers , 14 types, 30 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-GGD / | #7: Chemical | ChemComp-BCL / #8: Chemical | ChemComp-LDA / #9: Chemical | #10: Chemical | ChemComp-PO4 / | #11: Chemical | #12: Chemical | ChemComp-FE / | #13: Chemical | #14: Chemical | ChemComp-SPO / | #15: Chemical | ChemComp-CDL / | #16: Chemical | ChemComp-PC1 / | #17: Chemical | ChemComp-MG / | |
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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: 5.46 Å3/Da / Density % sol: 77.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1 M potassium phosphate pH 7.4, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution; 1.5 M potassium phosphate reservoir solution , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→120.497 Å / Num. all: 48933 / Num. obs: 48933 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.098 / Net I/σ(I): 17.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→38.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.227 / SU ML: 0.161 / SU R Cruickshank DPI: 0.3415 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.246 / 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: 48.142 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→38.57 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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