+Open data
-Basic information
Entry | Database: PDB / ID: 5x3t | ||||||
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Title | VapBC from Mycobacterium tuberculosis | ||||||
Components |
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Keywords | ANTITOXIN/TOXIN / TA system / ANTITOXIN-TOXIN complex / RIBONUCLEASE | ||||||
Function / homology | Function and homology information positive regulation of growth / negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Kang, S.M. / Kim, D.H. / Yoon, H.J. / Lee, B.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides. Authors: Kang, S.M. / Kim, D.H. / Lee, K.Y. / Park, S.J. / Yoon, H.J. / Lee, S.J. / Im, H. / Lee, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x3t.cif.gz | 159.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x3t.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 5x3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x3t_validation.pdf.gz | 489.6 KB | Display | wwPDB validaton report |
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Full document | 5x3t_full_validation.pdf.gz | 497.6 KB | Display | |
Data in XML | 5x3t_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 5x3t_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/5x3t ftp://data.pdbj.org/pub/pdb/validation_reports/x3/5x3t | HTTPS FTP |
-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
#1: Protein | Mass: 7729.558 Da / Num. of mol.: 4 / Mutation: L50M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: vapB26, Rv0581 / Production host: Escherichia coli (E. coli) / References: UniProt: O53778 #2: Protein | Mass: 16782.594 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: vapC26, Rv0582 / Production host: Escherichia coli (E. coli) References: UniProt: O53779, Hydrolases; Acting on ester bonds #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.88 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Tacsimate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 49908 / % possible obs: 99.8 % / Redundancy: 24.6 % / Net I/σ(I): 70.2 |
Reflection shell | Resolution: 2.65→2.7 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→30.78 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.22 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→30.78 Å
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Refine LS restraints |
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LS refinement shell |
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