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- PDB-4nid: Crystal structure of AlkB protein with cofactors bound to dsDNA c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nid | ||||||
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Title | Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A | ||||||
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![]() | OXIDOREDUCTASE/DNA / DNA/RNA direct repair / jelly-roll fold / DNA/RNA demethylation repair / Fe(II) / 2-KG / OXIDOREDUCTASE-DNA complex | ||||||
Function / homology | ![]() response to methyl methanesulfonate / DNA oxidative demethylase / : / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair ...response to methyl methanesulfonate / DNA oxidative demethylase / : / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, C.X. / Yi, C.Q. | ||||||
![]() | ![]() Title: Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues. Authors: Zhu, C. / Yi, 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 | ![]() | 131.1 KB | Display | ![]() |
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PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 462.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nigC ![]() 4nihC ![]() 4niiC ![]() 3bieS 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: 22830.104 Da / Num. of mol.: 1 / Fragment: UNP residues 12-214 / Mutation: S129C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4073.779 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 335 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-AKG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG4000, 0.1 M sodium chloride, 0.05 M magnesium chloride, 0.1 M 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 | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 39644 / Num. obs: 39565 / % possible obs: 99.8 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 |
Reflection shell | Resolution: 1.55→1.61 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BIE Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.63 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.669 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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Refine LS restraints |
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