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Yorodumi- PDB-2hh1: Reaction centre from Rhodobacter sphaeroides strain R-26.1 comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hh1 | ||||||
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Title | Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylcholine | ||||||
Components | (Reaction center protein ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS/MEMBRANE PROTEIN / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / LIPID BINDING SITES / BROMINATED LIPID / MEMBRANE PROTEIN / PHOTOSYNTHESIS-MEMBRANE PROTEIN COMPLEX | ||||||
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: 2.55 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 | 2hh1.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hh1.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/2hh1 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/2hh1 | 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 , 13 types, 506 molecules
#4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-BCL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PC9 / ( | #9: Chemical | ChemComp-LDA / #10: Chemical | ChemComp-FE / | #11: Chemical | ChemComp-CDL / | #12: Chemical | ChemComp-K / | #13: Chemical | ChemComp-HTO / | #14: Chemical | ChemComp-PC7 / ( | #15: Chemical | #16: 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: 5.5 Å3/Da / Density % sol: 77.67 % |
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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: ESRF / Beamline: BM14 / Wavelength: 0.91929 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2005 / Details: mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91929 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→46.03 Å / Num. obs: 67857 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 16.1 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 5.8 / Num. unique all: 9812 / % 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: 2.55→46.03 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.583 / SU ML: 0.108 / 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: 0.227 / ESU R Free: 0.191 / 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 52.6
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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: 42.284 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→46.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 56.1051 Å / Origin y: 60.7275 Å / Origin z: 64.8981 Å
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Refinement TLS group |
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