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- PDB-3rzj: Duplex Interrogation by a Direct DNA Repair Protein in the Search... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rzj | ||||||
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Title | Duplex Interrogation by a Direct DNA Repair Protein in the Search of Damage | ||||||
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![]() | OXIDOREDUCTASE/DNA / PROTEIN-DNA COMPLEX / jelly-roll / demethylase / nucleus / OXIDOREDUCTASE-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yi, C. / Chen, B. / Qi, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C. / Dinner, A. / Yang, C. / He, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.9 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.5 KB | Display | ![]() |
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Full document | ![]() | 473.8 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rzgC ![]() 3rzhC ![]() 3rzkC ![]() 3rzlC ![]() 3rzmC ![]() 3s57C ![]() 3s5aC ![]() 3btxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23778.156 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-261 / Mutation: C67S, C165S, G169C, C192S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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: 3933.582 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 4000.624 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 47 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/XL3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/XL3.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-AKG / |
#6: Chemical | ChemComp-XL3 / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 5000, 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: ![]() ![]() ![]() |
Detector | Date: Jun 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→67.36 Å / Num. all: 15056 / Num. obs: 14950 / % possible obs: 99.3 % / Observed criterion σ(F): 4.2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.3 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3BTX Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.916 / SU B: 19.062 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 4.2 / ESU R Free: 0.264 / 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: 52.094 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 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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