+Open data
-Basic information
Entry | Database: PDB / ID: 6ec7 | ||||||
---|---|---|---|---|---|---|---|
Title | Glutamylation domain, TbtB, from thiomuracin biosynthesis | ||||||
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 / Lantibiotic dehydratase domain protein Function and homology information | ||||||
Biological species | Thermobispora bispora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ec7.cif.gz | 175.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ec7.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ec7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/6ec7 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6ec7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6Y502 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M ammonium citrate pH 7.0, 15% PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.151→105.764 Å / Num. obs: 48860 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.151→2.188 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2405 / CC1/2: 0.893 / Rpim(I) all: 0.265 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.15→105.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.955 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 50.606 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→105.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|