+Open data
-Basic information
Entry | Database: PDB / ID: 5xe2 | |||||||||
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Title | Endoribonuclease from Mycobacterial species | |||||||||
Components | Endoribonuclease MazF4 | |||||||||
Keywords | HYDROLASE / endonuclease | |||||||||
Function / homology | Function and homology information negative regulation of DNA topoisomerase (ATP-hydrolyzing) activity / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | |||||||||
Authors | Ahn, D.-H. / Lee, K.-Y. / Lee, S.J. / Yoon, H.J. / Kim, S.-J. / Lee, B.-J. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural analyses of the MazEF4 toxin-antitoxin pair in Mycobacterium tuberculosis provide evidence for a unique extracellular death factor. Authors: Ahn, D.H. / Lee, K.Y. / Lee, S.J. / Park, S.J. / Yoon, H.J. / Kim, S.J. / 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 | 5xe2.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xe2.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xe2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xe2_validation.pdf.gz | 417.7 KB | Display | wwPDB validaton report |
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Full document | 5xe2_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | 5xe2_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 5xe2_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xe2 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xe2 | HTTPS FTP |
-Related structure data
Related structure data | 5xe3SC 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: 11697.274 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: mazF4, mazF-mt7, Rv1495, MTCY277.17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P9WII5, Hydrolases; Acting on ester bonds |
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#2: 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: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 0.2M sodium malonate at pH 7.0 and 20% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.01→30 Å / Num. obs: 7261 / % possible obs: 97.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.054 / Rrim(I) all: 0.157 / Χ2: 1.923 / Net I/σ(I): 5.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XE3 Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.373 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.171 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.44 Å2 / Biso mean: 23.868 Å2 / Biso min: 12.97 Å2
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Refinement step | Cycle: final / Resolution: 2.01→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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