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Yorodumi- PDB-2wx5: Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wx5 | ||||||
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Title | Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides reaction centre | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / REACTION CENTER / MEMBRANE PROTEIN / PHOTOSYNTHETIC REACTION CENTER / ELECTRON TRANSPORT / BACTERIOCHLOROPHYLL / IRON / MEMBRANE / MAGNESIUM / TRANSPORT / CHROMOPHORE / CHLOROPHYLL / METAL-BINDING / TRANSMEMBRANE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Marsh, M. / Frolov, D. / Crouch, L.I. / Fyfe, P.K. / Robert, B. / van Grondelle, R. / Jones, M.R. / Hadfield, A.T. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural and Spectroscopic Consequences of Hexa-Coordination of a Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre Authors: Frolov, D. / Marsh, M. / Crouch, L.I. / Fyfe, P.K. / Robert, B. / van Grondelle, R. / Hadfield, A.T. / Jones, M.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wx5.cif.gz | 213.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wx5.ent.gz | 164.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/2wx5 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/2wx5 | HTTPS FTP |
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-Related structure data
Related structure data | 1aigS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules H
#1: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): FL181R / References: UniProt: P0C0Y7, UniProt: Q3J170*PLUS |
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-REACTION CENTRE PROTEIN ... , 2 types, 2 molecules LM
#2: Protein | Mass: 31356.408 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: PHE 181 MUTATED TO ARG, BACTERIOCHLOROPHYLL HEXA COORDINATE Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): FL181R / References: UniProt: P0C0Y8, UniProt: Q3J1A5*PLUS |
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#3: Protein | Mass: 34398.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): FL181R / References: UniProt: P0C0Y9, UniProt: Q3J1A6*PLUS |
-Non-polymers , 11 types, 315 molecules
#4: Chemical | ChemComp-LDA / #5: Chemical | #6: Chemical | ChemComp-BCL / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-CDL / | #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-SPN / | #13: Chemical | ChemComp-U10 / | #14: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 5.6 Å3/Da / Density % sol: 78 % / Description: NONE |
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Crystal grow | pH: 8 Details: MOTHER LIQUOR AT 9 MG/ML OF THE AM149W REACTION CENTRE, 0.09% V/V LDAO, 3.5% W/V HEPTANE-1, 2,3-TRIOL AND 0.65 M POTASSIUM PHOSPHATE (PH 8.0) WERE EQUILIBRATED AGAINST A RESERVOIR SOLUTION ...Details: MOTHER LIQUOR AT 9 MG/ML OF THE AM149W REACTION CENTRE, 0.09% V/V LDAO, 3.5% W/V HEPTANE-1, 2,3-TRIOL AND 0.65 M POTASSIUM PHOSPHATE (PH 8.0) WERE EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 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: 0.97 |
Detector | Date: Nov 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→44.54 Å / Num. obs: 61876 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.63→2.78 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.5 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AIG Resolution: 2.63→20.4 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.305 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.268 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.291 Å2
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Refinement step | Cycle: LAST / Resolution: 2.63→20.4 Å
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Refine LS restraints |
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