+Open data
-Basic information
Entry | Database: PDB / ID: 5zil | |||||||||
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Title | Crystal structure of bacteriorhodopsin at 1.29 A resolution | |||||||||
Components | Bacteriorhodopsin | |||||||||
Keywords | PROTON TRANSPORT / proton pump / 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 / Resolution: 1.29 Å | |||||||||
Authors | Hasegawa, N. / Jonotsuka, H. / Miki, K. / Takeda, K. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: X-ray structure analysis of bacteriorhodopsin at 1.3 angstrom resolution. Authors: Hasegawa, N. / Jonotsuka, H. / Miki, K. / Takeda, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zil.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zil.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/5zil ftp://data.pdbj.org/pub/pdb/validation_reports/zi/5zil | HTTPS FTP |
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-Related structure data
Related structure data | 5zimC 5zinC 1c3wS S: Starting model for refinement C: citing same article (ref.) |
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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: 25061.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile) Strain: ATCC 700922 / JCM 11081 / NRC-1 / References: UniProt: P02945 | ||
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#2: Chemical | ChemComp-RET / | ||
#3: Chemical | ChemComp-L2P / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / Details: MO, 2.0-2.5 M PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 15 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.065 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.29→47.421 Å / Num. obs: 57755 / % possible obs: 99.9 % / Redundancy: 5.551 % / Biso Wilson estimate: 21.618 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.069 / Χ2: 0.972 / Net I/σ(I): 13.41 / Num. measured all: 320609 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C3W Resolution: 1.29→47.421 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 63.14 Å2 / Biso mean: 23.1674 Å2 / Biso min: 11.86 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→47.421 Å
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