+Open data
-Basic information
Entry | Database: PDB / ID: 1o0a | ||||||
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Title | BACTERIORHODOPSIN L INTERMEDIATE AT 1.62 A RESOLUTION | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / SERPENTINE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Lanyi, J.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Mechanism of proton transport in bacteriorhodopsin from crystallographic structures of the K, L, M1, M2, and M2' intermediates of the photocycle. Authors: Lanyi, J.K. / Schobert, B. | ||||||
History |
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Remark 300 | BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT TWO CONFORMATIONS OF THE WILD- ... BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT TWO CONFORMATIONS OF THE WILD-TYPE PROTEIN. MODEL 1 IS THE L INTERMEDIATE WITH OCCUPANCY OF 0.60 WHILE MODEL 2 IS THE NON-ILLUMINATED BACTERIORHODOPSIN (BR STATE) WITH OCCUPANCY OF 0.40. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o0a.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o0a.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 1o0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o0a ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o0a | HTTPS FTP |
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-Related structure data
Related structure data | 1m0lS 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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Number of models | 2 |
-Components
#1: Protein | Mass: 26929.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / Gene: BOP / Plasmid: PRN2367 / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 | ||||
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#2: Chemical | ChemComp-RET / | ||||
#3: Chemical | ChemComp-LI1 / #4: Chemical | ChemComp-SQU / | #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: 1.77 Å3/Da / Density % sol: 42.38 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: cubic lipid phase / pH: 5.6 Details: POTASSIUM [PHOSPHATE, pH 5.60, CUBIC LIPID PHASE, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.6 / 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: ALS / Beamline: 8.2.1 / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Jun 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→25 Å / Num. all: 28181 / Num. obs: 28097 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.058 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 1.62→1.69 Å / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.4 / % possible all: 88.9 |
Reflection | *PLUS Num. measured all: 572564 |
Reflection shell | *PLUS % possible obs: 88.9 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M0L Resolution: 1.62→25 Å / Num. parameters: 8325 / Num. restraintsaints: 19687 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 230 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2073.02 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→25 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.144 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.185 / Rfactor Rwork: 0.132 |