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Yorodumi- PDB-3hap: Crystal structure of bacteriorhodopsin mutant L111A crystallized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hap | ||||||
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Title | Crystal structure of bacteriorhodopsin mutant L111A crystallized from bicelles | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | TRANSPORT PROTEIN / bacteriorhodopsin / packing force / van der Waals / evolutionary constraint / membrane protein / integral membrane protein / helical membrane protein / proton transport / Cell membrane / Chromophore / Hydrogen ion transport / Ion transport / Membrane / Photoreceptor protein / Pyrrolidone carboxylic acid / Receptor / Retinal protein / Sensory transduction / Transmembrane / Transport | ||||||
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: 1.6 Å | ||||||
Authors | Joh, N.H. / Yang, D. / Bowie, J.U. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Similar energetic contributions of packing in the core of membrane and water-soluble proteins. Authors: Joh, N.H. / Oberai, A. / 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 | 3hap.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hap.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/3hap ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3hap | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26887.420 Da / Num. of mol.: 1 / Mutation: L111A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / Strain (production host): L33 / References: UniProt: P02945 |
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-Non-polymers , 8 types, 171 molecules
#2: Chemical | ChemComp-RET / | ||||||||||||
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#3: Chemical | ChemComp-D12 / #4: Chemical | ChemComp-D10 / #5: Chemical | ChemComp-R16 / | #6: Chemical | ChemComp-CPS / | #7: Chemical | ChemComp-HP6 / | #8: Chemical | ChemComp-DD9 / | #9: 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: 2.73 Å3/Da / Density % sol: 54.99 % |
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Crystal grow | Temperature: 310 K / Method: hanging drop, bicelle method / pH: 4 Details: 400ul 4M NaPi, 30ul 6M 1,6-hexanediol, 35ul 100% triethylene glycol, 535 ul H2O, pH 4.0, hanging drop, bicelle method, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9998 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 36787 / % possible obs: 93.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Χ2: 1.031 / Net I/σ(I): 22.431 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.382 / Num. unique all: 3007 / Χ2: 1.026 / % possible all: 78.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→21.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.843 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.084 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.4 Å2 / Biso mean: 19.588 Å2 / Biso min: 8.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→21.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.644 Å / Total num. of bins used: 20
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