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- PDB-8i6d: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i6d | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form VI | ||||||
![]() | Uracil-DNA glycosylase | ||||||
![]() | HYDROLASE/INHIBITOR / DNA repair / Base excision repair / Inhibitor-complex / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
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 | ![]() ![]() | ||||||
![]() | Raj, P. / Paul, A. / Gopal, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the ...Title: Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment. Authors: Kesharwani, S. / Raj, P. / Paul, A. / Roy, K. / Bhanot, A. / Mehta, A. / Gopal, A. / Varshney, U. / Gopal, B. / Sundriyal, S. #1: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.5 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.2 KB | Display | ![]() |
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Full document | ![]() | 481 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i61C ![]() 8i62C ![]() 8i63C ![]() 8i64C ![]() 8i65C ![]() 8i66C ![]() 8i67C ![]() 8i68C ![]() 8i69C ![]() 8i6aC ![]() 8i6bC ![]() 8i6cC ![]() 4ws4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25813.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ung, Rv2976c, MTCY349.11 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 0.1 M Tris pH 6.5, 1.4 M Sodium citrate, 15% PEG (w/v) 3350, 2% Benzamidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25.61 Å / Num. obs: 15539 / % possible obs: 96.28 % / Redundancy: 2 % / CC1/2: 0.973 / Rmerge(I) obs: 0.1249 / Net I/σ(I): 5.55 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 0.391 / Num. unique obs: 1513 / CC1/2: 0.667 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WS4 Resolution: 2.4→25.61 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.136 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 1.184 / ESU R Free: 0.326 / 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: 17.162 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→25.61 Å
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Refine LS restraints |
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