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Yorodumi- PDB-6kw0: The structure of EanB/Y353F-Cys412-persulfide in tetrahedral inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kw0 | ||||||
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Title | The structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with ergothioneine | ||||||
Components | Sulfurtransferase | ||||||
Keywords | TRANSFERASE / intermediate / mutant / ergothioneine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlorobium limicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Wu, L. / Liu, P.H. / Zhou, J.H. | ||||||
Citation | Journal: To Be Published Title: The structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with ergothioneine Authors: Wu, L. / Liu, P.H. / Zhou, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kw0.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kw0.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/6kw0 ftp://data.pdbj.org/pub/pdb/validation_reports/kw/6kw0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52218.137 Da / Num. of mol.: 2 / Mutation: Y353F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium limicola (bacteria) / Strain: DSM 245 / NBRC 103803 / 6330 / Gene: Clim_1149 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: B3ECE3 |
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-Non-polymers , 6 types, 22 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES/imidazole pH6.5 0.03 M of each halide 12.5% PEG1000 12.5%PEG3350 12.5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 23952 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.245 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.79→2.84 Å / Rmerge(I) obs: 1.614 / Num. unique obs: 1182 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.8→49 Å
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