+Open data
-Basic information
Entry | Database: PDB / ID: 1s8j | ||||||
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Title | Nitrate-bound D85S mutant of bacteriorhodopsin | ||||||
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 | 1s8j.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s8j.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 1s8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/1s8j ftp://data.pdbj.org/pub/pdb/validation_reports/s8/1s8j | HTTPS FTP |
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-Related structure data
Related structure data | 1s8lC 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 / Species (production host): Halobacterium salinarum / Production host: Halobacterium sp. NRC-1 (Halophile) / References: UniProt: P02945 | ||
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#2: Chemical | ChemComp-NO3 / | ||
#3: Chemical | ChemComp-RET / | ||
#4: Chemical | ChemComp-LI1 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.69 % |
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-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→60 Å / Num. all: 160242 / Num. obs: 11603 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.147 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.3→2.44 Å / Num. unique all: 1638 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JV7 Resolution: 2.3→11.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1866063.8 / 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: 41.0826 Å2 / ksol: 0.410085 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→11.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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