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Yorodumi- PDB-2oxm: Crystal structure of a UNG2/modified DNA complex that represent a... -
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-Basic information
Entry | Database: PDB / ID: 2oxm | ||||||
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Title | Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping | ||||||
Components |
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Keywords | Hydrolase/DNA / ENZYME DNA COMPLEX / UNG2 / URACIL DNA GLYCOSYLASE / Hydrolase-DNA COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bianchet, M.A. / Krosky, D.J. / Stivers, J.T. / Amzel, L.M. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Authors: Parker, J.B. / Bianchet, M.A. / Krosky, D.J. / Friedman, J.I. / Amzel, L.M. / Stivers, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oxm.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oxm.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxm ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxm | HTTPS FTP |
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-Related structure data
Related structure data | 2oytC 1emhS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: DNA chain | Mass: 2711.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetically made References: Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: DNA chain | Mass: 3066.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetically made |
#3: 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 |
#4: 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: 2.48 Å3/Da / Density % sol: 50.45 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: A solution of human UNG2 (22 mg/ml) in 50 mM Tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M duplex DNA (2.5 mM)m incubate at room Temperature for 30 min. and then ...Details: A solution of human UNG2 (22 mg/ml) in 50 mM Tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M duplex DNA (2.5 mM)m incubate at room Temperature for 30 min. and then centrifugate at 10000 g for 5 min.Co-crystallizarion condition were 22% PEG 4000, 100 MM HEPES pH 6.5 and 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 11, 2006 / Details: Osmic Mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 12024 / Num. obs: 11434 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.5 / Redundancy: 4.1 % / Biso Wilson estimate: 50.583 Å2 / Rsym value: 0.162 / Χ2: 2.784 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.91 / Num. unique all: 1046 / Rsym value: 0.59 / Χ2: 1.834 / % possible all: 89.4 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMH Resolution: 2.5→29.5 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.846 / SU B: 9.116 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.757 / ESU R Free: 0.382 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.756 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.517 Å / Total num. of bins used: 20
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