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Yorodumi- PDB-1ogv: Lipidic cubic phase crystal structure of the photosynthetic react... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ogv | ||||||
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Title | Lipidic cubic phase crystal structure of the photosynthetic reaction centre from Rhodobacter sphaeroides | ||||||
Components | (Reaction center protein ...Photosynthetic reaction centre) x 3 | ||||||
Keywords | REACTION CENTRE / PHOTOSYNTHESIS / CHARGE SEPARATION / INTEGRAL MEMBRANE PROTEIN / LIPID / ELECTRON TRANSPORT / BACTERIOCHLOROPHYLL / TRANSMEMBRANE | ||||||
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: 2.35 Å | ||||||
Authors | Katona, G. / Andreasson, U. / Landau, E.M. / Andreasson, L.-E. / Neutze, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Lipidic Cubic Phase Crystal Structure of the Photosynthetic Reaction Centre from Rhodobacter Sphaeroides at 2.35 A Resolution Authors: Katona, G. / Andreasson, U. / Landau, E.M. / Andreasson, L.-E. / Neutze, 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 | 1ogv.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogv.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ogv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogv ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogv | HTTPS FTP |
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-Related structure data
Related structure data | 1aijS 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
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 27042.123 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 11-260 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P0C0Y7 |
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#2: Protein | Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P0C0Y9 |
-Non-polymers , 7 types, 146 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | ChemComp-U10 / | #7: Chemical | ChemComp-CDL / | #8: Chemical | ChemComp-FE2 / | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
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-Details
Compound details | FUNCTION: THE REACTION CENTER IS A MEMBRANE-BOUND COMPLEX THAT MEDIATES THE INITIAL PHOTOCHEMICAL ...FUNCTION: THE REACTION CENTER IS A MEMBRANE-BOUND COMPLEX THAT MEDIATES THE INITIAL PHOTOCHEMI |
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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: 2.8 Å3/Da / Density % sol: 55.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: lipidic cubic phase / pH: 7.5 Details: 60% MONOOLEIN/40% 25 MG/ML PROT. +(4:1)18% JEFFAMINE M-600, 1M HEPES PH7.5, 0.7M AMM.SULF., pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: solid cubic phase | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 5, 2002 / Details: GE MIRROR |
Radiation | Monochromator: DIAMOND C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→42.3 Å / Num. obs: 49134 / % possible obs: 96.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.8 / % possible all: 97.6 |
Reflection | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 42.3 Å / Num. obs: 51199 / Redundancy: 7.2 % / Rmerge(I) obs: 0.115 |
Reflection shell | *PLUS % possible obs: 97.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AIJ Resolution: 2.35→42.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3182284.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 79.2016 Å2 / ksol: 0.460079 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→42.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 42.3 Å / Num. reflection obs: 51199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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