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Yorodumi- PDB-2hj6: Reaction centre from Rhodobacter sphaeroides strain R-26.1 comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hj6 | ||||||
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Title | Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylserine | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | PHOTOSYNTHESIS/MEMBRANE PROTEIN / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / LIPID BINDING SITES / BROMINATED LIPIDS / MEMBRANE PROTEIN / PHOTOSYNTHESIS-MEMBRANE PROTEIN COMPLEX | ||||||
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: 3 Å | ||||||
Authors | Roszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Brominated Lipids Identify Lipid Binding Sites on the Surface of the Reaction Center from Rhodobacter sphaeroides. Authors: Roszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hj6.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hj6.ent.gz | 164.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/2hj6 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/2hj6 | 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: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid. Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y8 |
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#2: Protein | Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid. Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y9 |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid. Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y7 |
-Non-polymers , 12 types, 376 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FE / | #8: Chemical | #9: Chemical | ChemComp-HTO / | #10: Chemical | ChemComp-CDL / | #11: Chemical | ChemComp-PS2 / | #12: Chemical | ChemComp-LDA / #13: Chemical | #14: Chemical | ChemComp-K / | #15: 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: 5.47 Å3/Da / Density % sol: 77.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Potassium phosphate, LDAO, 1,2,3-heptanetriol, 1,2,3-hexanetriol, dioxane, NaCl, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.92 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 20, 2005 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.29 Å / Num. obs: 41533 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 81.1 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 7 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6031 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Unpublished structure of reaction centre at 1.95A resolution Resolution: 3→39.29 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.834 / SU B: 23.187 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: TLS thermal mode followed by the restrained refinement of atomic coordinates and isotropic B-factors; all details in the pdb-file Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.502 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; the above average isotropic B value is an average residual B after TLS refinement while the final average atomic B is 70.2
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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: 57.076 Å2
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Refinement step | Cycle: LAST / Resolution: 3→39.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 55.6813 Å / Origin y: 60.7673 Å / Origin z: 64.4424 Å
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Refinement TLS group |
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