+Open data
-Basic information
Entry | Database: PDB / ID: 1m0m | ||||||
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Title | BACTERIORHODOPSIN M1 INTERMEDIATE AT 1.43 A RESOLUTION | ||||||
Components | BACTERIORHODOPSIN | ||||||
Keywords | ION 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: 1.43 Å | ||||||
Authors | Lanyi, J.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle. Authors: Lanyi, J. / Schobert, B. | ||||||
History |
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Remark 300 | BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT THE TWO CONFORMATIONS OF THE WILD- ...BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT THE TWO CONFORMATIONS OF THE WILD-TYPE PROTEIN. MODEL 1 IS THE BR STATE WITH OCCUPANCY OF 0.40 AND MODEL 2 IS THE MI STATE WITH OCCUPANCY OF 0.60. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m0m.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m0m.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0m ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0m | HTTPS FTP |
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-Related structure data
Related structure data | 1c3wS 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: 28270.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / 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: 1.81 Å3/Da / Density % sol: 41.3 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: cubic lipid phase / pH: 5.6 Details: cubic lipid phase with mono-olein and potassium phosphate, pH 5.60, CUBIC LIPID PHASE, temperature 295K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.6 Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532. | |||||||||||||||||||||||||
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: 5.0.2 / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Aug 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→25 Å / Num. obs: 39522 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.43→1.47 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.5 / % possible all: 96.6 |
Reflection | *PLUS Highest resolution: 1.43 Å / Lowest resolution: 25 Å / Num. measured all: 517904 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3W Resolution: 1.43→25 Å / Num. parameters: 8453 / Num. restraintsaints: 8759 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: MEROHEDRAL TWINNING RATIO OF 52:48
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Refine analyze | Num. disordered residues: 21 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2070.9 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→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 all: 0.1644 / Rfactor obs: 0.1631 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.163 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.43 Å / Lowest resolution: 1.47 Å / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.142 |