+Open data
-Basic information
Entry | Database: PDB / ID: 1p8i | ||||||
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Title | F219L BACTERIORHODOPSIN MUTANT | ||||||
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: 1.86 Å | ||||||
Authors | Lanyi, J.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystallographic Structures of the M and N Intermediates of Bacteriorhodopsin: Assembly of a Hydrogen-Bonded Chain of Water Molecules between Asp-96 and the Retinal Schiff Base Authors: Schobert, B. / Brown, L.S. / 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 | 1p8i.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8i.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8i ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8i | HTTPS FTP |
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-Related structure data
Related structure data | 1p8hC 1p8uC 1m0lS 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: 26895.484 Da / Num. of mol.: 1 / Mutation: F219L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / Gene: BOP OR VNG1467G / 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: 1.82 Å3/Da / Density % sol: 32.3 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: cubic lipid phase / pH: 5.6 Details: MONO-OLEIN, POTASSIUM PHOSPHATE, pH 5.60, CUBIC LIPID PHASE, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / 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: SSRL / Beamline: BL9-1 / Wavelength: 0.93 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Dec 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→25 Å / Num. all: 21424 / Num. obs: 21424 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.084 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.86→1.93 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 3.4 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 1.86 Å / Lowest resolution: 25 Å / Num. measured all: 492763 |
Reflection shell | *PLUS % possible obs: 98 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M0L Resolution: 1.86→25 Å / Num. parameters: 8292 / Num. restraintsaints: 8216 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2072 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→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: 0.22 / Rfactor Rwork: 0.191 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.86 Å / Lowest resolution: 1.93 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.17 |