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Yorodumi- PDB-3rzm: Duplex Interrogation by a Direct DNA Repair Protein in the Search... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rzm | ||||||
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Title | Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage | ||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / PROTEIN-DNA COMPLEX / JELLY-ROLL / DEMETHYLASE / NUCLEUS / 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: 3.06 Å | ||||||
Authors | Yi, C. / Chen, B. / Qi, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C. / Dinner, A. / Yang, C. / 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 | 3rzm.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rzm.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 3rzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/3rzm ftp://data.pdbj.org/pub/pdb/validation_reports/rz/3rzm | HTTPS FTP |
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-Related structure data
Related structure data | 3rzgC 3rzhC 3rzjC 3rzkC 3rzlC 3s57C 3s5aC 3btxS 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
#1: Protein | Mass: 23446.746 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-260 / Mutation: C67S, C165S, G169C, C192S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH2, ABH2 / Production host: Escherichia coli (E. coli) 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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#2: DNA chain | Mass: 3990.622 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-XL3 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 4000, 0.1M SODIUM CHLORIDE, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.54 Å |
Detector | Date: Apr 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→50 Å / Num. all: 9740 / Num. obs: 9613 / % possible obs: 98.7 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.06→3.17 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BTX Resolution: 3.06→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / SU B: 32.402 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 2.2 / ESU R Free: 0.434 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.353 Å2
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Refinement step | Cycle: LAST / Resolution: 3.06→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.06→3.139 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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