+Open data
-Basic information
Entry | Database: PDB / ID: 4in5 | ||||||
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Title | (M)L214G mutant of the Rhodobacter sphaeroides Reaction Center | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Saer, R.G. / Hardjasa, A. / Murphy, M.E. / 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 HA and BA 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 | 4in5.cif.gz | 210.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4in5.ent.gz | 163.1 KB | Display | PDB format |
PDBx/mmJSON format | 4in5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4in5 ftp://data.pdbj.org/pub/pdb/validation_reports/in/4in5 | HTTPS FTP |
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-Related structure data
Related structure data | 4in6C 4in7C 2j8cS C: citing same article (ref.) 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
-Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31477.584 Da / Num. of mol.: 1 / Mutation: L214G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: pufL, puhA / Plasmid: pRS1::(M)L214G / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y8, UniProt: Q3J1A5*PLUS |
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#2: Protein | Mass: 34359.527 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 / Plasmid: pRS1::(M)L214G / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y9, UniProt: Q3J1A6*PLUS |
#3: 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: pufL, puhA / Plasmid: pRS1::(M)L214G / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P0C0Y7, UniProt: Q3J170*PLUS |
-Non-polymers , 12 types, 227 molecules
#4: Chemical | ChemComp-LDA / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-SPO / | #13: Chemical | ChemComp-PC1 / | #14: Chemical | ChemComp-K / | #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: 5.45 Å3/Da / Density % sol: 77.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution, 1.52 M potassium phosphate reservoir solution, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 19, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator (DCM) with indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→120.472 Å / Num. all: 105008 / Num. obs: 105008 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.084 / Net I/σ(I): 11.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J8C Resolution: 2.2→55.62 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.212 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1401 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.127 / 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: 44.899 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→55.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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