+Open data
-Basic information
Entry | Database: PDB / ID: 1m0k | ||||||
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Title | BACTERIORHODOPSIN K 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 light-driven active monoatomic ion transmembrane transporter activity / 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 K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. Authors: Schobert, B. / Cupp-Vickery, J. / Hornak, V. / Smith, S. / Lanyi, J. | ||||||
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 non-illuminated BACTERIORHODOPSIN (BR STATE) with the occupancy of 0.60 while Model 2 is the K INTERMEDIATE (K STATE) with the occupancy of 0.40. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m0k.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m0k.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 1m0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m0k_validation.pdf.gz | 860.1 KB | Display | wwPDB validaton report |
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Full document | 1m0k_full_validation.pdf.gz | 892.6 KB | Display | |
Data in XML | 1m0k_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1m0k_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0k ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0k | HTTPS FTP |
-Related structure data
Related structure data | 1m0lC 1c3wS 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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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 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: 1.84 Å3/Da / Density % sol: 42.06 % | |||||||||||||||||||||||||
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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, 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: 41822 / % possible obs: 96.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.037 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.43→1.48 Å / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.4 / % possible all: 89.4 |
Reflection | *PLUS Highest resolution: 1.43 Å / Lowest resolution: 25 Å / Num. measured all: 608447 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 89.4 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.4 |
-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: 8359 / Num. restraintsaints: 8618 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: MEROHEDRAL TWINNING RATIO OF 51:49
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Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2073 | |||||||||||||||||||||||||||||||||
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 obs: 0.134 / Rfactor Rfree: 0.176 / Rfactor Rwork: 0.134 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.43 Å / Lowest resolution: 1.48 Å / Rfactor Rfree: 0.166 / Rfactor Rwork: 0.127 |