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- PDB-4h9l: Bacterial Photosynthetic Reaction Center from Rhodobacter sphaero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h9l | ||||||
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Title | Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides with ILE M265 replaced with SER | ||||||
![]() | (Reaction center protein ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / cofactors / quinone-protein interactions / photosynthetic reaction center / electron transfer / primary quinone / QA | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Mattis, A.J. / Wraight, C.A. | ||||||
![]() | ![]() Title: Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides Authors: Mattis, A.J. / Wraight, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193 KB | Display | ![]() |
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PDB format | ![]() | 148.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h99C ![]() 4hbhC ![]() 4hbjC ![]() 1pcrS 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: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 35201.336 Da / Num. of mol.: 1 / Mutation: I265S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 108 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FE / | #8: Chemical | ChemComp-SPO / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.74 Å3/Da / Density % sol: 78.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: drop: 14 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 3.2% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH ...Details: drop: 14 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 3.2% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.77→121.408 Å / Num. obs: 53634 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.93 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.77 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PCR Resolution: 2.77→19.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.332 / SU ML: 0.168 / Stereochemistry target values: ML Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.77→2.84 Å
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