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Yorodumi- PDB-6vba: Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vba | |||||||||
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Title | Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA) | |||||||||
Components | Uracil-DNA glycosylase | |||||||||
Keywords | HYDROLASE / GLYCOSYLASE / DNA REPAIR / URACIL REMOVAL FROM DNA / ALPHA/ BETA PROTEIN / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Moiani, D. / Arvai, A.S. / Tainer, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Prog.Biophys.Mol.Biol. / Year: 2021 Title: An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. Authors: Nguyen, M.T. / Moiani, D. / Ahmed, Z. / Arvai, A.S. / Namjoshi, S. / Shin, D.S. / Fedorov, Y. / Selvik, E.J. / Jones, D.E. / Pink, J. / Yan, Y. / Laverty, D.J. / Nagel, Z.D. / Tainer, J.A. / Gerson, S.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vba.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vba.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vba ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vba | HTTPS FTP |
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-Related structure data
Related structure data | 1akzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25544.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P13051, uracil-DNA glycosylase |
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#2: Chemical | ChemComp-QU4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2mM TRIS pH 8.5, 20 mM Mgcl2, 21% PEG8000, ATA inhibitor was co-crystallized with the UDG protein with a concentration of circa 4mM in solution |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979458 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979458 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.45 Å / Num. obs: 247193 / % possible obs: 94.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 18.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 1.127 / Num. unique obs: 19459 / CC1/2: 0.656 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AKZ Resolution: 1.8→35.45 Å / SU ML: 0.2727 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.5442 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.45 Å
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Refine LS restraints |
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LS refinement shell |
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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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