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Yorodumi- PDB-3zum: Photosynthetic Reaction Centre Mutant with Phe L146 replaced with Ala -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zum | ||||||
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Title | Photosynthetic Reaction Centre Mutant with Phe L146 replaced with Ala | ||||||
Components | (REACTION CENTER PROTEIN ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / ELECTRON TRANSFER / PRIMARY CHARGE SEPARATION / CHARGE RECOMBINATION / TRANSIENT ABSORPTION SPECTROSCOPY | ||||||
Function / homology | Function and homology information 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 | RHODOBACTER SPHAEROIDES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å | ||||||
Authors | Gibasiewicz, K. / Pajzderska, M. / Potter, J.A. / Fyfe, P.K. / Dobek, A. / Brettel, K. / Jones, M.R. | ||||||
Citation | Journal: J Phys Chem B / Year: 2011 Title: Mechanism of Recombination of the P(+)H(A)(-) Radical Pair in Mutant Rhodobacter Sphaeroides Reaction Centers with Modified Free Energy Gaps between P(+)B(A)(-) and P(+)H(A)(-). Authors: Gibasiewicz, K. / Pajzderska, M. / Potter, J.A. / Fyfe, P.K. / Dobek, A. / Brettel, K. / Jones, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zum.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zum.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zum_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 3zum_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 3zum_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 3zum_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/3zum ftp://data.pdbj.org/pub/pdb/validation_reports/zu/3zum | HTTPS FTP |
-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 HLM
#1: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: P0C0Y7 |
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#2: Protein | Mass: 31270.295 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 34398.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: P0C0Y9 |
-Non-polymers , 8 types, 225 molecules
#4: Chemical | #5: Chemical | ChemComp-LDA / #6: Chemical | ChemComp-BCL / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-FE / | #10: Chemical | ChemComp-SPN / | #11: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.75 Å3/Da / Density % sol: 78 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop Details: VAPOUR DIFFUSION, SITTING DROP, 0.09% LDAO, 3.5% 1,2,3 HEPTANETRIOL, 0.75 M POTASSIUM PHOSPHATE PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: 14.1 / Type: SRS / Wavelength: 1.488 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→119 Å / Num. obs: 68081 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.08 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.5→119.52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.25 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES M303-307, H1-10, H246-260 WERE NOT LOCATED IN THE STRUCTURE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.731 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→119.52 Å
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Refine LS restraints |
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