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Yorodumi- PDB-2c2p: The crystal structure of mismatch specific uracil-DNA glycosylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c2p | ||||||
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Title | The crystal structure of mismatch specific uracil-DNA glycosylase (MUG) from Deinococcus radiodurans | ||||||
Components | G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE | ||||||
Keywords | HYDROLASE / DEINOCOCCUS RADIODURANS / RADIATION RESISTANCE / DNA REPAIR ENZYMES / URACIL-DNA GLYCOSYLASE / MISMATCH SPECIFIC DNA-GLYCOSYLASE / MUG | ||||||
Function / homology | Function and homology information pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / uracil DNA N-glycosylase activity Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Moe, E. / Leiros, I. / Smalas, A.O. / McSweeney, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The Crystal Structure of Mismatch Specific Uracil-DNA Glycosylase (Mug) from Deinococcus Radiodurans Reveals a Novel Catalytic Residue and Broad Substrate Specificity Authors: Moe, E. / Leiros, I. / Smalas, A.O. / Mcsweeney, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c2p.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c2p.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c2p ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c2p | HTTPS FTP |
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-Related structure data
Related structure data | 2c2qC 1mugS C: citing same article (ref.) 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: 21785.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACETATE BOUND IN THE SUBSTRATE POCKET Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9RWF4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | pH: 6.5 Details: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30% W/V PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939272 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939272 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→12 Å / Num. obs: 22686 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MUG Resolution: 1.75→87.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.32 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6 AND 190-199 WERE DISORDERED AND THEREFORE NOT MODELLED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→87.71 Å
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Refine LS restraints |
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