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Yorodumi- PDB-4nid: Crystal structure of AlkB protein with cofactors bound to dsDNA c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nid | ||||||
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Title | Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A | ||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / DNA/RNA direct repair / jelly-roll fold / DNA/RNA demethylation repair / Fe(II) / 2-KG / OXIDOREDUCTASE-DNA complex | ||||||
Function / homology | Function and homology information response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair / oxidative demethylation / DNA demethylation / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Zhu, C.X. / Yi, C.Q. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nid.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nid.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/4nid ftp://data.pdbj.org/pub/pdb/validation_reports/ni/4nid | HTTPS FTP |
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-Related structure data
Related structure data | 4nigC 4nihC 4niiC 3bieS 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
-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.) Escherichia coli (E. coli) / Gene: alkB, aidD, b2212, JW2200 / Production host: Escherichia coli (E. coli) / References: UniProt: P05050, DNA oxidative demethylase |
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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
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-AKG / |
#6: 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: 2.54 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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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