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Yorodumi- PDB-7clj: Crystal structure of Thermoplasmatales archaeon heliorhodopsin E1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7clj | ||||||
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Title | Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant | ||||||
Components | heliorhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / Alpha-helical | ||||||
Function / homology | Heliorhodopsin / Heliorhodopsin / identical protein binding / membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Heliorhodopsin HeR Function and homology information | ||||||
Biological species | Thermoplasmatales archaeon SG8-52-1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tanaka, T. / Shihoya, W. / Yamashita, K. / Nureki, O. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structural basis for unique color tuning mechanism in heliorhodopsin. Authors: Tanaka, T. / Singh, M. / Shihoya, W. / Yamashita, K. / Kandori, H. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7clj.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7clj.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 7clj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7clj_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7clj_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7clj_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7clj_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/7clj ftp://data.pdbj.org/pub/pdb/validation_reports/cl/7clj | HTTPS FTP |
-Related structure data
Related structure data | 6is6S S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3871080 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29872.273 Da / Num. of mol.: 1 / Mutation: E108D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasmatales archaeon SG8-52-1 (archaea) Gene: AYK20_03510 / Plasmid: pET21a (+) / Production host: Escherichia coli (E. coli) / Variant (production host): C41 (Rosetta) / References: UniProt: A0A151EDA9 | ||||||
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#2: Chemical | ChemComp-RET / | ||||||
#3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 25% PEG 350 MME, 100mM Na-citrate, 100mM ammonium sulfate or lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→30 Å / Num. obs: 9975 / % possible obs: 99.1 % / Redundancy: 7.71 % / CC1/2: 0.982 / Rrim(I) all: 0.38 / Net I/σ(I): 5.36 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6is6 Resolution: 2.6→28.368 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.881 / SU B: 16.319 / SU ML: 0.326 / Cross valid method: FREE R-VALUE / ESU R: 1.428 / ESU R Free: 0.368 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.753 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→28.368 Å
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Refine LS restraints |
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LS refinement shell |
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