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Yorodumi- PDB-1q5i: Crystal structure of bacteriorhodopsin mutant P186A crystallized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q5i | ||||||
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Title | Crystal structure of bacteriorhodopsin mutant P186A crystallized from bicelles | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / alpha helix | ||||||
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: 2.3 Å | ||||||
Authors | Yohannan, S. / Faham, S. / Yang, D. / Whitelegge, J.P. / Bowie, J.U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Authors: Yohannan, S. / Faham, S. / Yang, D. / Whitelegge, J.P. / Bowie, J.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q5i.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q5i.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/1q5i ftp://data.pdbj.org/pub/pdb/validation_reports/q5/1q5i | HTTPS FTP |
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-Related structure data
Related structure data | 1q5jC 1py6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26903.463 Da / Num. of mol.: 2 / Mutation: P186A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Strain: L33 / Gene: BOP OR VNG1467G / Plasmid: pMPK85 / Production host: Escherichia coli (E. coli) / References: UniProt: P02945 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4 Details: DMPC, CHAPSO, sodium phosphate, hexanediol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 310.0K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3.7 / Method: unknown | ||||||||||||||||||||||||||||
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: 8.2.2 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2003 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→500 Å / Num. obs: 24112 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PY6 Resolution: 2.3→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Crystal twinning was observed. Twinning operation = -h, -k, h+l. Twinning fraction = 0.5
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→500 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.3 Å
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.255 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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