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Yorodumi- PDB-6ktv: The structure of EanB complex with hercynine and persulfided Cys412 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ktv | ||||||
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Title | The structure of EanB complex with hercynine and persulfided Cys412 | ||||||
Components | Sulfurtransferase | ||||||
Keywords | TRANSFERASE / complex / persulfide | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlorobium limicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wu, L. / Liu, P.H. / Zhou, J.H. | ||||||
Citation | Journal: Acs Catalysis / Year: 2020 Title: Single-Step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis Authors: Cheng, R. / Wu, L. / Lai, R. / Peng, C. / Naowarojna, N. / Hu, W. / Li, X. / Whelan, S.A. / Lee, N. / Lopez, J. / Zhao, C. / Yong, Y. / Xue, J. / Jiang, X. / Grinstaff, M.W. / Deng, Z. / ...Authors: Cheng, R. / Wu, L. / Lai, R. / Peng, C. / Naowarojna, N. / Hu, W. / Li, X. / Whelan, S.A. / Lee, N. / Lopez, J. / Zhao, C. / Yong, Y. / Xue, J. / Jiang, X. / Grinstaff, M.W. / Deng, Z. / Chen, J. / Cui, Q. / Zhou, J.H. / Liu, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ktv.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ktv.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ktv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/6ktv ftp://data.pdbj.org/pub/pdb/validation_reports/kt/6ktv | HTTPS FTP |
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-Related structure data
Related structure data | 6ktwC 6ktxSC 6ktzC 6ku1C 6ku2C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52266.203 Da / Num. of mol.: 1 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 , 11 types, 265 molecules
#2: Chemical | ChemComp-AVJ / | ||||||||||||||||
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#3: Chemical | ChemComp-MG / | ||||||||||||||||
#4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-PG4 / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-NI / | #12: Water | ChemComp-HOH / | |
-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: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M MES/imidazole pH6.5, 0.02M of each alcohol, 10%PEG20k, 20%PEG550MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 31581 / % possible obs: 99.8 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 1.041 / Num. unique obs: 1530 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KTX Resolution: 2.2→45.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.2→45.7 Å
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LS refinement shell | Resolution: 2.198→2.269 Å /
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