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- PDB-8i6b: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i6b | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form I | ||||||
![]() | 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 | ![]() | 67.8 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8i61C ![]() 8i62C ![]() 8i63C ![]() 8i64C ![]() 8i65C ![]() 8i66C ![]() 8i67C ![]() 8i68C ![]() 8i69C ![]() 8i6aC ![]() 8i6cC ![]() 8i6dC ![]() 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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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 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 291 molecules ![](data/chem/img/ODF.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ODF / | ||||||
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#3: Chemical | ChemComp-EDO / | ||||||
#4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-NA / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
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: 38.97 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.5 / Details: 0.1 M Tris pH 5.5, 25% PEG (w/v) 3350 |
-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: Jul 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30.49 Å / Num. obs: 25418 / % possible obs: 93.72 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0368 / Net I/σ(I): 11.77 |
Reflection shell | Resolution: 1.6→1.657 Å / Rmerge(I) obs: 0.1443 / Num. unique obs: 2415 / CC1/2: 0.927 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WS4 Resolution: 1.6→30.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / 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: 11.572 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→30.49 Å
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Refine LS restraints |
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