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Yorodumi- PDB-1s8l: Anion-free form of the D85S mutant of bacteriorhodopsin from crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s8l | ||||||
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Title | Anion-free form of the D85S mutant of bacteriorhodopsin from crystals grown in the presence of halide | ||||||
Components | Bacteriorhodopsin precursor | ||||||
Keywords | MEMBRANE PROTEIN / bacteriorhodopsin / anion / pump | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Halobacterium sp. (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Facciotti, M.T. / Cheung, V.S. / Lunde, C.S. / Rouhani, S. / Baliga, N.S. / Glaeser, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Specificity of anion binding in the substrate pocket of bacteriorhodopsin. Authors: Facciotti, M.T. / Cheung, V.S. / Lunde, C.S. / Rouhani, S. / Baliga, N.S. / Glaeser, R.M. | ||||||
History |
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Remark 600 | HETEROGEN ONLY A SMALL PORTION OF HET GROUP LI1 WAS MODELED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s8l.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s8l.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 1s8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/1s8l ftp://data.pdbj.org/pub/pdb/validation_reports/s8/1s8l | HTTPS FTP |
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-Related structure data
Related structure data | 1s8jC 1jv7S C: citing same article (ref.) 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: 26901.490 Da / Num. of mol.: 1 / Mutation: D85S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium sp. (Halophile) / Gene: BOP, VNG1467G / Genus (production host): Halobacterium / Production host: Halobacterium (Halophile) / References: UniProt: P02945 | ||
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#2: Chemical | ChemComp-RET / | ||
#3: Chemical | ChemComp-LI1 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 4.6 Details: sodium acetate, PEG 4000, KCl, pH 4.6, lipidic cubic phase, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1272 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47 Å / Num. all: 111430 / Num. obs: 10515 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.103 |
Reflection shell | Resolution: 2.3→2.44 Å / Rsym value: 0.199 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JV7 Resolution: 2.3→46.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1887275.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.1448 Å2 / ksol: 0.377968 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→46.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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