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- PDB-4wpl: Crystal structure of Mycobacterium tuberculosis uracil-DNA glycos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wpl | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with uracil, 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 | ![]() | 120.5 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 470.9 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wpkC ![]() 4wruC ![]() 4wrvC ![]() 4wrwC ![]() 4wrxC ![]() 4wryC ![]() 4wrzC ![]() 4ws0C ![]() 4ws1C ![]() 4ws2C ![]() 4ws3C ![]() 4ws4C ![]() 4ws5C ![]() 4ws6C ![]() 4ws7C ![]() 4ws8C ![]() 3a7nS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 6 types, 252 molecules ![](data/chem/img/URA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-URA / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 4.6 Details: Ammonium acetate, sodium acetate trihydrate, PEG 4000, hexafluoro 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→19.83 Å / Num. obs: 70859 / % possible obs: 98 % / Redundancy: 3 % / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.6 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A7N Resolution: 1.15→19.83 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.834 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / 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: 11.387 Å2
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Refinement step | Cycle: 1 / Resolution: 1.15→19.83 Å
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Refine LS restraints |
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