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Yorodumi- PDB-4y9h: The 1.43 angstrom crystal structure of bacteriorhodopsin crystall... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y9h | |||||||||
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Title | The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles | |||||||||
Components | Bacteriorhodopsin | |||||||||
Keywords | LIPID BINDING PROTEIN / bacteriorhodopsin / complex / membrane protein / Cell membrane / Multi-pass membrane protein | |||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / monoatomic ion channel activity / protein domain specific binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Halobacterium salinarum (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | |||||||||
Authors | Saiki, H. / Sugiyama, S. / Kakinouchi, K. / Kawatake, S. / Hanashima, S. / Matsumori, N. / Murata, M. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles Authors: Saiki, H. / Sugiyama, S. / Kakinouchi, K. / Kawatake, S. / Hanashima, S. / Matsumori, N. / Murata, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9h.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9h.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9h ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9h | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24760.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) (Halophile) Strain: ATCC 29341 / DSM 671 / R1 / References: UniProt: B0R5N9 |
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-Non-polymers , 8 types, 111 molecules
#2: Chemical | ChemComp-RET / | ||||||||
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#3: Chemical | ChemComp-PO4 / | ||||||||
#4: Chemical | ChemComp-HP6 / | ||||||||
#5: Chemical | ChemComp-D12 / #6: Chemical | ChemComp-D10 / #7: Chemical | ChemComp-R16 / | #8: Chemical | ChemComp-DD9 / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 180mM 1,6-hexanediol, 2.6M NaH2PO4, 3.5% triethyleneglycol, pH4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→50 Å / Num. obs: 55216 / % possible obs: 99.4 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.675 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.844 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→50 Å
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