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Yorodumi- PDB-6wp8: Proton-pumping mutant of Mastigocladopsis repens rhodopsin chlori... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wp8 | ||||||
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Title | Proton-pumping mutant of Mastigocladopsis repens rhodopsin chloride pump | ||||||
Components | Proton-pumping rhodopsin chloride pump | ||||||
Keywords | MEMBRANE PROTEIN / retinal protein / proton pump / ion pump | ||||||
Function / homology | RETINAL Function and homology information | ||||||
Biological species | Mastigocladopsis repens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Besaw, J.E. / Ernst, O.P. / Ou, W. / Morizumi, T. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants. Authors: Besaw, J.E. / Ou, W.L. / Morizumi, T. / Eger, B.T. / Sanchez Vasquez, J.D. / Chu, J.H.Y. / Harris, A. / Brown, L.S. / Miller, R.J.D. / Ernst, O.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wp8.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wp8.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/6wp8 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/6wp8 | HTTPS FTP |
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-Related structure data
Related structure data | 6xl3C 6nwf 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: 27145.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mastigocladopsis repens (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-RET / |
#3: Sugar | ChemComp-BOG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.31 % |
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Crystal grow | Temperature: 307.15 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 3.6 M sodium phosphate monobasic monohydrate, pH 4.0, 180 mM 1,6 hexanediol, 3.5% triethylene glycol PH range: 4.0-4.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.92 Å / Num. obs: 11125 / % possible obs: 92 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.5 Å2 / CC1/2: 0.98 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1275 / CC1/2: 0.3 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NWF 6nwf Resolution: 2.5→28.92 Å / SU ML: 0.2918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3279 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.92 Å
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Refine LS restraints |
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LS refinement shell |
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