+Open data
-Basic information
Entry | Database: PDB / ID: 3s5a | ||||||
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Title | ABH2 cross-linked to undamaged dsDNA-2 with cofactors | ||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / Jelly-roll fold / dioxygenase / DNA Binding / cross-linking / 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 / oxidative demethylation / DNA demethylation / ferrous iron binding ...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 / oxidative demethylation / DNA demethylation / ferrous iron binding / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yi, C. / Chen, B. / Qi, B. / Ramirez, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C.Q. / Dinner, A.R. / Yang, C.-G. / He, C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Duplex interrogation by a direct DNA repair protein in search of base damage Authors: Yi, C. / Chen, B. / Qi, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C.J. / Dinner, A.R. / Yang, C.G. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s5a.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s5a.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 3s5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/3s5a ftp://data.pdbj.org/pub/pdb/validation_reports/s5/3s5a | HTTPS FTP |
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-Related structure data
Related structure data | 3rzgC 3rzhC 3rzjC 3rzkC 3rzlC 3rzmC 3s57C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23267.611 Da / Num. of mol.: 1 / Fragment: dioxygenase domain (UNP RESIDUES 56-258) / Mutation: C67S, C165S, C192S, G169C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABH2, ALKBH2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / 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 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4222.740 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 4313.831 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 344 molecules
#4: Chemical | ChemComp-MN / | ||||
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#5: Chemical | ChemComp-AKG / | ||||
#6: Chemical | #7: Chemical | ChemComp-XL3 / | #8: 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: 2.87 Å3/Da / Density % sol: 57.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 12% PEG 8000, 100mM sodium chloride, 50mM Magnesium chloride, 100mM cacodylate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 52281 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2 / Num. unique all: 5173 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.591 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.109 / 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: 32.871 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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