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Yorodumi- PDB-3mbv: Structure of bacterirhodopsin crystallized in betta-XylOC(16+4) m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mbv | ||||||
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Title | Structure of bacterirhodopsin crystallized in betta-XylOC(16+4) meso phase | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Borshchevskiy, V. / Moiseeva, E. / Kuklin, A. / Bueldt, G. / Hato, M. / Gordeliy, V. | ||||||
Citation | Journal: J.Cryst.Growth / Year: 2010 Title: Isoprenoid-chained lipid beta-XylOC16+4 A novel molecule for in meso membrane protein crystallization Authors: Borshchevskiy, V. / Moiseeva, E. / Kuklin, A. / Bueldt, G. / Hato, M. / Gordeliy, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mbv.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mbv.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/3mbv ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mbv | HTTPS FTP |
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-Related structure data
Related structure data | 1c3wS 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
#1: Protein | Mass: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP residues 14-261 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: S9 / References: UniProt: P02945 |
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#2: Chemical | ChemComp-RET / |
#3: Chemical | ChemComp-BXC / ( |
#4: Water | ChemComp-HOH / |
Nonpolymer details | LIGAND BXC IS REFERENCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 298 K / Method: in meso crystallization / Details: in meso crystallization, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2005 | |||||||||||||||
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→53.13 Å / Num. all: 13746 / Num. obs: 13746 / % possible obs: 87.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.2 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1989 / % possible all: 87 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3W Resolution: 2→47.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.755 / SU ML: 0.1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.034 / 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 max: 66.63 Å2 / Biso mean: 21.068 Å2 / Biso min: 5.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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