+Open data
-Basic information
Entry | Database: PDB / ID: 5ukh | ||||||
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Title | Structure of TelC from Streptococcus intermedius B196 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Antibacterial effector protein / Lipid II phosphatase / Type VII secretion / Esx secretion | ||||||
Function / homology | LXG domain / LXG domain of WXG superfamily / LXG domain profile. / metal ion binding / LXG domain-containing protein Function and homology information | ||||||
Biological species | Streptococcus intermedius B196 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å | ||||||
Authors | Whitney, J.C. / Ching, M.Q. / Bryant, D. / Mougous, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2017 Title: A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. Authors: Whitney, J.C. / Peterson, S.B. / Kim, J. / Pazos, M. / Verster, A.J. / Radey, M.C. / Kulasekara, H.D. / Ching, M.Q. / Bullen, N.P. / Bryant, D. / Goo, Y.A. / Surette, M.G. / Borenstein, E. / ...Authors: Whitney, J.C. / Peterson, S.B. / Kim, J. / Pazos, M. / Verster, A.J. / Radey, M.C. / Kulasekara, H.D. / Ching, M.Q. / Bullen, N.P. / Bryant, D. / Goo, Y.A. / Surette, M.G. / Borenstein, E. / Vollmer, W. / Mougous, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ukh.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ukh.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ukh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/5ukh ftp://data.pdbj.org/pub/pdb/validation_reports/uk/5ukh | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41935.555 Da / Num. of mol.: 1 / Fragment: UNP residues 201-552 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius B196 (bacteria) Gene: SIR_1489 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZG69 | ||
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#2: Chemical | #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: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium Acetate pH 4.6, 0.1 M CaCl2, 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→49.2 Å / Num. obs: 34824 / % possible obs: 100 % / Redundancy: 25.6 % / Net I/σ(I): 11.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.98→49.2 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→49.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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