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Yorodumi- PDB-2c53: A comparative study of uracil DNA glycosylases from human and her... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c53 | ||||||
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Title | A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1 | ||||||
Components | URACIL DNA GLYCOSYLASE | ||||||
Keywords | HYDROLASE / URACIL DNA GLYCOSYLASE / DNA REPAIR / DNA DAMAGE / GLYCOSIDASE | ||||||
Function / homology | Function and homology information uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / host cell nucleus Similarity search - Function | ||||||
Biological species | HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Krusong, K. / Carpenter, E.P. / Bellmy, S.R.W. / Savva, R. / Baldwin, G.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: A Comparative Study of Uracil-DNA Glycosylases from Human and Herpes Simplex Virus Type 1. Authors: Krusong, K. / Carpenter, E.P. / Bellamy, S.R.W. / Savva, R. / Baldwin, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c53.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c53.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/2c53 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/2c53 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27341.418 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1) Plasmid: D88N/H20N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10186, uridine nucleosidase | ||||
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#2: Chemical | ChemComp-DUR / | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Compound details | CUTS URACIL RESIDUES FROM THE DNA. ENGINEERED RESIDUE IN CHAIN A, ASP 178 TO ASN ENGINEERED RESIDUE ...CUTS URACIL RESIDUES FROM THE DNA. ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.1 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 19411 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.83 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.27 / % possible all: 63.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→14.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 688666.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 1 - 16 IN THIS MOLECULE DO NOT APPEAR IN THE ELECTRON DENSITY AND ARE PRESUMED TO BE DISORDERED.
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 77.4854 Å2 / ksol: 0.397766 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→14.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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