[English] 日本語
Yorodumi- PDB-4wav: Crystal Structure of Haloquadratum walsbyi bacteriorhodopsin muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wav | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Haloquadratum walsbyi bacteriorhodopsin mutant D93N | ||||||
Components | Bacteriorhodopsin-I | ||||||
Keywords | TRANSPORT PROTEIN / Bacteriorhodopsin / proton pump / Membrane protein | ||||||
Function / homology | Function and homology information : / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Haloquadratum walsbyi C23 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Wang, A.H.J. / Hsu, M.F. / Yang, C.S. / Fu, H.Y. | ||||||
Funding support | Taiwan, 1items
| ||||||
Citation | Journal: To be published Title: Crystal structure of an acid-tolerant light-driven proton pump at 1.85 Angstroms resolution Authors: Hsu, M.F. / Fu, H.Y. / Cai, C.J. / Yi, S.P. / Yang, C.S. / Wang, A.H.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wav.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wav.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/4wav ftp://data.pdbj.org/pub/pdb/validation_reports/wa/4wav | HTTPS FTP |
---|
-Related structure data
Related structure data | 1vgoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28505.104 Da / Num. of mol.: 2 / Mutation: D93N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloquadratum walsbyi C23 (archaea) / Gene: bop1, Hqrw_1016 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: G0LFX8 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: calcium chloride, HEPES, PEG 400 |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Type: OTHER / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 3, 2013 / Details: Inter-Frame | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Fixed-Exit Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. obs: 11796 / % possible obs: 97.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.149 / Χ2: 0.925 / Net I/av σ(I): 12.621 / Net I/σ(I): 5.7 / Num. measured all: 72386 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VGO Resolution: 2.8→26.12 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2392 / WRfactor Rwork: 0.1816 / FOM work R set: 0.8414 / SU B: 12.122 / SU ML: 0.247 / SU Rfree: 0.4402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 78.17 Å2 / Biso mean: 27.78 Å2 / Biso min: 5.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→26.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.802→2.874 Å / Total num. of bins used: 20
|