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Yorodumi- PDB-5lse: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH Glu L212 replaced with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lse | |||||||||
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Title | PHOTOSYNTHETIC REACTION CENTER MUTANT WITH Glu L212 replaced with Ala (CHAIN L, EL212W), Asp L213 replaced with ALA (Chain L, DL213A) AND LEU M215 REPLACED WITH ALA (CHAIN M, LM215A) | |||||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | |||||||||
Keywords | ELECTRON TRANSPORT / TRANSMEMBRANE / PHOTOSYNTHESIS | |||||||||
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: 2.5 Å | |||||||||
Authors | Fyfe, P.K. / Jones, M.R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Biochim.Biophys.Acta / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lse.cif.gz | 350.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lse.ent.gz | 298 KB | Display | PDB format |
PDBx/mmJSON format | 5lse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/5lse ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lse | HTTPS FTP |
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-Related 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: 31244.346 Da / Num. of mol.: 1 / Mutation: EL212A, DL213A Source method: isolated from a genetically manipulated source Details: Glu L212 to Ala engineered mutation Asp L213 to Ala engineered mutation Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides (bacteria) / Variant (production host): EL212A/DL213A/LM215A / References: UniProt: P0C0Y8 |
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#2: Protein | Mass: 34356.461 Da / Num. of mol.: 1 / Mutation: LM215A Source method: isolated from a genetically manipulated source Details: Leu M215 ALA engineered mutation / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: pRKEH10D / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y9 |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Missing N and C-terminal residues unobserved in electron density Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Plasmid: PRKEH10D / Production host: Rhodobacter sphaeroides (bacteria) / Variant (production host): EL212A/DL213A/LM215A / References: UniProt: P0C0Y7 |
-Non-polymers , 10 types, 290 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-D12 / #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-SPN / | #10: Chemical | #11: Chemical | ChemComp-PO4 / | #12: Chemical | ChemComp-CDL / | #13: 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: 5.2 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: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→23.9 Å / Num. obs: 70501 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILD TYPE RHODOBACTER SPHAEROIDES COORDINATES (Unpublished data) Resolution: 2.5→23.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.34 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.171 / 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: 50.22 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→23.9 Å
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