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Open data
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Basic information
Entry | Database: PDB / ID: 4in5 | ||||||
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Title | (M)L214G mutant of the Rhodobacter sphaeroides Reaction Center | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | OXIDOREDUCTASE / Electron Transfer / Chromatophore | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saer, R.G. / Hardjasa, A. / Murphy, M.E. / Beatty, J.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.5 KB | Display | ![]() |
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PDB format | ![]() | 163.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4in6C ![]() 4in7C ![]() 2j8cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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.) ![]() ![]() |
#3: Protein | Mass: 28895.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 12 types, 227 molecules ![](data/chem/img/LDA.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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