+Open data
-Basic information
Entry | Database: PDB / ID: 1c8r | ||||||
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Title | BACTERIORHODOPSIN D96N BR STATE AT 2.0 A RESOLUTION | ||||||
Components | PROTEIN (BACTERIORHODOPSIN) | ||||||
Keywords | PROTON TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / D96N BR STATE / ION TRANSPORT / MEROHEDRAL TWINNING | ||||||
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 / ISOMORPHOUS / Resolution: 1.8 Å | ||||||
Authors | Luecke, H. | ||||||
Citation | Journal: Science / Year: 1999 Title: Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Authors: Luecke, H. / Schobert, B. / Richter, H.T. / Cartailler, J.P. / Lanyi, J.K. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Structure of Bacteriorhodopsin at 1.55 Angstrom Resolution Authors: Luecke, H. / Schobert, B. / Richter, H.-T. / Cartailler, J.-P. / Lanyi, J.K. #2: Journal: Science / Year: 1998 Title: Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution Authors: Luecke, H. / Richter, H.-T. / Lanyi, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c8r.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8r.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8r ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8r | HTTPS FTP |
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-Related structure data
Related structure data | 1c8sC 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: 26928.516 Da / Num. of mol.: 1 / Fragment: "BR" STATE INTERMEDIATE / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 301 (C15) DIETHER LIPID BILAYER Source: (gene. exp.) Halobacterium salinarum (Halophile) / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 | ||||||
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#2: Chemical | ChemComp-LI1 / #3: Chemical | ChemComp-SQU / | #4: Chemical | ChemComp-RET / | #5: 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: 2.13 Å3/Da / Density % sol: 42.26 % | ||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: cubic lipid phase / pH: 5.6 Details: MO:WATER:PHOSPHATE, pH 5.6, CUBIC LIPID PHASE, temperature 296K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: other / Details: Gabriele, R., (1998) J. Struct. Biol., 121, 82. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1 |
Detector | Type: ADSC / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 19005 / % possible obs: 88.1 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 5.4 / % possible all: 87.5 |
Reflection | *PLUS Num. measured all: 167219 |
Reflection shell | *PLUS % possible obs: 87.5 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS Starting model: PDB ENTRY 1C3W Resolution: 1.8→12 Å / Num. parameters: 8308 / Num. restraintsaints: 8229 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: MEROHEDRAL TWINNING RATIO OF 53:47
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Solvent computation | Solvent model: SHELXL-97 SWAT, BABINET'S PRINCIPLE | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→12 Å
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Refine LS restraints |
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