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Yorodumi- PDB-8i6b: Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycos... -
+Open data
-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 | ||||||
Components | Uracil-DNA glycosylase | ||||||
Keywords | HYDROLASE/INHIBITOR / DNA repair / Base excision repair / Inhibitor-complex / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Raj, P. / Paul, A. / Gopal, B. | ||||||
Funding support | India, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 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: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i6b.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i6b.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 8i6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i6b_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 8i6b_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 8i6b_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 8i6b_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/8i6b ftp://data.pdbj.org/pub/pdb/validation_reports/i6/8i6b | HTTPS FTP |
-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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: ung, Rv2976c, MTCY349.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFQ9, uracil-DNA glycosylase |
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-Non-polymers , 6 types, 291 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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