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Yorodumi- PDB-4ws0: Crystal structure of Mycobacterium tuberculosis uracil-DNA glycos... -
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-Basic information
Entry | Database: PDB / ID: 4ws0 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-fluorouracil (A), Form II | ||||||
Components | Uracil-DNA glycosylase | ||||||
Keywords | HYDROLASE / DNA-repair / Excision repair / Conformational selection / Ligand-binding | ||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.974 Å | ||||||
Authors | Arif, S.M. / Geethanandan, K. / Mishra, P. / Surolia, A. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications. Authors: Arif, S.M. / Geethanandan, K. / Mishra, P. / Surolia, A. / Varshney, U. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands. Authors: Kaushal, P.S. / Talawar, R.K. / Varshney, U. / Vijayan, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources. Authors: Kaushal, P.S. / Talawar, R.K. / Krishna, P.D. / Varshney, U. / Vijayan, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG. Authors: Saikrishnan, K. / Bidya Sagar, M. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M. #4: Journal: Nucleic Acids Res. / Year: 1998 Title: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG. Authors: Ravishankar, R. / Bidya Sagar, M. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ws0.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ws0.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ws0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ws0_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 4ws0_full_validation.pdf.gz | 443.5 KB | Display | |
Data in XML | 4ws0_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 4ws0_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/4ws0 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/4ws0 | HTTPS FTP |
-Related structure data
Related structure data | 4wpkC 4wplC 4wruC 4wrvC 4wrwC 4wrxC 4wryC 4wrzC 4ws1C 4ws2C 4ws3C 4ws4C 4ws5C 4ws6C 4ws7C 4ws8C 3a7nS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25813.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ung, Rv2976c, MTCY349.11 / Plasmid: pRSETB MTUUDG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WFQ9, uracil-DNA glycosylase | ||||
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#2: Chemical | ChemComp-URF / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / | #5: 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: 1.97 Å3/Da / Density % sol: 37.64 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: Sodium acetate trihydrate, Tris HCl, PEG 4000, 1,3-butanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→36.89 Å / Num. obs: 14239 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.9 / % possible all: 91.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A7N Resolution: 1.974→36.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.829 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.165 / 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: 13.051 Å2
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Refinement step | Cycle: 1 / Resolution: 1.974→36.89 Å
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