+Open data
-Basic information
Entry | Database: PDB / ID: 4wxd | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis OGT-R37K | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / DNA damage reversal / alkylated DNA-protein alkyltransferase / DNA-protein complex | ||||||
Function / homology | Function and homology information methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / response to nitrosative stress / DNA alkylation repair / methylation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Miggiano, R. / Rossi, F. / Garavaglia, S. / Rizzi, M. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Biochem.J. / Year: 2016 Title: Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA. Authors: Miggiano, R. / Perugino, G. / Ciaramella, M. / Serpe, M. / Rejman, D. / Pav, O. / Pohl, R. / Garavaglia, S. / Lahiri, S. / Rizzi, M. / Rossi, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wxd.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wxd.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 4wxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wxd_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 4wxd_full_validation.pdf.gz | 422.9 KB | Display | |
Data in XML | 4wxd_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4wxd_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/4wxd ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wxd | HTTPS FTP |
-Related structure data
Related structure data | 4wx9C 4wxcC 4bhbS 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: 17836.143 Da / Num. of mol.: 1 / Mutation: I2V, R37K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ogt, Rv1316c, MTCY130.01c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WJW5, methylated-DNA-[protein]-cysteine S-methyltransferase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 4% PEG8000, 4% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→34.6 Å / Num. all: 50946 / Num. obs: 8668 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 8.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BHB Resolution: 2.3→34.6 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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