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- PDB-3a7n: Crystal structure of uracil-DNA glycosylase from Mycobacterium tu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a7n | ||||||
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Title | Crystal structure of uracil-DNA glycosylase from Mycobacterium tuberculosis | ||||||
![]() | Uracil-DNA glycosylase | ||||||
![]() | HYDROLASE / Ung-Ugi interactions / Ung-DNA complex / citrate as protein ligand / ligand binding / inhibitor design / DNA damage / DNA repair / Glycosidase | ||||||
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 | ![]() ![]() | ||||||
![]() | Kaushal, P.S. / Talawar, R.K. / Varshney, U. / Vijayan, M. | ||||||
![]() | ![]() 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. #1: ![]() 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.V. / Varshney, U. / Vijayan, M. #2: ![]() 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. #3: ![]() 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 | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 45.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zhxS 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
#1: Protein | Mass: 25813.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37RV / Gene: ung, Rv2976c / Plasmid: PRSETB MTUUDG / Production host: ![]() ![]() References: UniProt: P67071, UniProt: P9WFQ9*PLUS, uridine nucleosidase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 1.8M tri-ammonium citrate pH 7.0, 10% isopropanol, microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2008 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 18628 / Num. obs: 18238 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2583 / Rsym value: 0.493 / % possible all: 97.7 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZHX Resolution: 1.95→26.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.309 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.059 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→26.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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