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- PDB-4wpk: Crystal structure of Mycobacterium tuberculosis uracil-DNA glycos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wpk | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase, Form I | ||||||
![]() | Uracil-DNA glycosylase | ||||||
![]() | HYDROLASE / DNA-repair / Excision repair / Conformational selection / Ligand-binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Arif, S.M. / Geethanandan, K. / Mishra, P. / Surolia, A. / Varshney, U. / Vijayan, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.7 KB | Display | ![]() |
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PDB format | ![]() | 92.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.1 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wplC ![]() 4wruC ![]() 4wrvC ![]() 4wrwC ![]() 4wrxC ![]() 4wryC ![]() 4wrzC ![]() 4ws0C ![]() 4ws1C ![]() 4ws2C ![]() 4ws3C ![]() 4ws4C ![]() 4ws5C ![]() 4ws6C ![]() 4ws7C ![]() 4ws8C ![]() 3a7nS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() Gene: ung, Rv2976c, MTCY349.11 / Plasmid: pRSETB MTUUDG / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.5 / Details: 1.6 M Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72932 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→23.74 Å / Num. obs: 115505 / % possible obs: 100 % / Redundancy: 4.9 % / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 0.98→1.03 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Starting model: 3A7N Resolution: 0.98→23.74 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.68 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / 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: 12.14 Å2
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Refinement step | Cycle: 1 / Resolution: 0.98→23.74 Å
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Refine LS restraints |
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