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Yorodumi- PDB-6ec8: Glutamylation domain, TbtB, from thiomuracin biosynthesis bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ec8 | ||||||
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Title | Glutamylation domain, TbtB, from thiomuracin biosynthesis bound to 5'-phosphodesmethylglutamycin | ||||||
Components | Lantibiotic dehydratase domain protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / RiPP / thiopeptide / thiomuracin / tRNA-dependent / glutamylation / dehydratase | ||||||
Function / homology | Lantibiotic dehydratase, N-terminal / Lantibiotic dehydratase, N terminus / Chem-J4G / Lantibiotic dehydratase domain protein Function and homology information | ||||||
Biological species | Thermobispora bispora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å | ||||||
Authors | Cogan, D.P. / Nair, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics. Authors: Bothwell, I.R. / Cogan, D.P. / Kim, T. / Reinhardt, C.J. / van der Donk, W.A. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ec8.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ec8.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ec8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ec8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ec8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ec8_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 6ec8_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/6ec8 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6ec8 | HTTPS FTP |
-Related structure data
Related structure data | 6ec7SC 6m7yC 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: 96006.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) (bacteria) Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51 Gene: Tbis_0550 Variant: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51 Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6Y502 |
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#2: Chemical | ChemComp-J4G / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M ammonium sulfate, 15% PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.148→96.1 Å / Num. obs: 48184 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.148→2.185 Å / Rmerge(I) obs: 0.727 / Num. unique obs: 2366 / CC1/2: 0.877 / Rpim(I) all: 0.311 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EC7 Resolution: 2.148→71 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.535 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.935 Å2
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Refinement step | Cycle: 1 / Resolution: 2.148→71 Å
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Refine LS restraints |
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