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Yorodumi- PDB-3bty: Crystal structure of human ABH2 bound to dsDNA containing 1meA th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bty | ||||||
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Title | Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site | ||||||
Components |
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Keywords | Oxidoreductase/DNA / protein/DNA interaction / human dioxygenase / DNA repair / cross-linking / DNA damage / Iron / Metal-binding / Nucleus / Oxidoreductase / Oxidoreductase-DNA COMPLEX | ||||||
Function / homology | Function and homology information cytosine C-5 DNA demethylase activity / ALKBH2 mediated reversal of alkylation damage / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / rDNA binding / DNA alkylation repair / ferrous iron binding / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Yang, C.-G. / Yi, C. / He, C. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Authors: Yang, C.G. / Yi, C. / Duguid, E.M. / Sullivan, C.T. / Jian, X. / Rice, P.A. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bty.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bty.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 3bty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bty_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 3bty_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 3bty_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3bty_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/3bty ftp://data.pdbj.org/pub/pdb/validation_reports/bt/3bty | HTTPS FTP |
-Related structure data
Related structure data | 3bi3C 3bieC 3bkzC 3btxC 3btzC 3bu0C 3bucC 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: 3981.631 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 23136.414 Da / Num. of mol.: 1 / Mutation: C67S, C165S, C192S, G169C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: 12q24.11 / Gene: ALKBH2, ABH2 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6NS38, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
#4: Chemical | ChemComp-XL3 / |
#5: 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: 3.19 Å3/Da / Density % sol: 61.43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8% PEG 8000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 17062 / Num. obs: 17062 / % possible obs: 95.6 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.2 / Num. unique all: 860 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.355 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.235 / 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: 50.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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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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