+Open data
-Basic information
Entry | Database: PDB / ID: 4xgr | ||||||
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Title | Crystal structure of addiction module from Mycobacterial species | ||||||
Components |
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Keywords | TOXIN/ANTITOXIN / Mycobacteria / addiction module / TOXIN-ANTITOXIN complex | ||||||
Function / homology | Function and homology information positive regulation of growth / negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Lee, B.-J. / Lee, I.-G. / Lee, S.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structural and functional studies of the Mycobacterium tuberculosis VapBC30 toxin-antitoxin system: implications for the design of novel antimicrobial peptides Authors: Lee, I.-G. / Lee, S.J. / Chae, S. / Lee, K.Y. / Kim, J.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 | 4xgr.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xgr.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xgr_validation.pdf.gz | 482.5 KB | Display | wwPDB validaton report |
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Full document | 4xgr_full_validation.pdf.gz | 487.4 KB | Display | |
Data in XML | 4xgr_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 4xgr_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/4xgr ftp://data.pdbj.org/pub/pdb/validation_reports/xg/4xgr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14585.790 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: vapC30, Rv0624, MTCY20H10.05 / Production host: Escherichia coli (E. coli) References: UniProt: P9WF77, Hydrolases; Acting on ester bonds #2: Protein | Mass: 9202.435 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: vapB30, Rv0623 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJ35 #3: Chemical | #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: 3.31 Å3/Da / Density % sol: 62.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M sodium citrate at pH 5.5, and 5% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97912 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.7→48.15 Å / Num. obs: 34963 / % possible obs: 98.9 % / Redundancy: 6.7 % / Net I/σ(I): 37.037 |
-Processing
Software |
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Refinement | Resolution: 2.7→48.15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.799 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.062 / 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: 59.969 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→48.15 Å
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Refine LS restraints |
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