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- PDB-5lri: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lri | |||||||||
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Title | PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH TRP (CHAIN L, EL212W) | |||||||||
![]() | (Reaction center protein ...) x 3 | |||||||||
![]() | ELECTRON TRANSPORT / TRANSMEMBRANE / PHOTOSYNTHESIS | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Fyfe, P.K. / Jones, M.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: On the mechanism of ubiquinone mediated photocurrent generation by a reaction center based photocathode. Authors: Friebe, V.M. / Swainsbury, D.J. / Fyfe, P.K. / van der Heijden, W. / Jones, M.R. / Frese, R.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 368.6 KB | Display | ![]() |
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PDB format | ![]() | 295.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 31403.486 Da / Num. of mol.: 1 / Mutation: E212W Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION EL212W Source: (gene. exp.) ![]() Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: pufL, RHOS4_18610, RSP_0257 / Plasmid: PRKEH10D / Production host: ![]() |
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#2: Protein | Mass: 34398.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: pufM, RHOS4_18600, RSP_0256 / Plasmid: PRKEH10D / Production host: ![]() |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: puhA, RHOS4_18960, RSP_0291 / Plasmid: PRKEH10D / Production host: ![]() |
-Non-polymers , 9 types, 311 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/DD9.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/DD9.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/SPN.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-LDA / #10: Chemical | ChemComp-SPN / | #11: Chemical | ChemComp-CDL / | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.2 Å3/Da / Density % sol: 74.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Well containing 9 mg mL-1 RC, 0.09 % v/v LDAO, 3.5 % w/v 1,2,3-heptanetriol, and 0.75 M potassium phosphate (pH 7.5) equilibrated against 1.5 M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→18 Å / Num. obs: 77800 / % possible obs: 95 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.63 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Wild Type RHODOBACTER SPHAEROIDESCOORDINATES (UNPUBLISHED DATA) Resolution: 2.4→17.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.229 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.125 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→17.91 Å
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Refine LS restraints |
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