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Yorodumi- PDB-3bi3: X-ray structure of AlkB protein bound to dsDNA containing 1meA/A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bi3 | ||||||
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Title | X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors | ||||||
Components |
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Keywords | Oxidoreductase/DNA / Dioxygenase / protein DNA interaction / alkylation repair / DNA damage / DNA repair / Iron / Metal-binding / Oxidoreductase / 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 / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / 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 | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yi, C. / Yang, C.-G. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Authors: Yang, C.G. / Yi, C. / Duguid, E.M. / Sullivan, C.T. / Jian, X. / Rice, P.A. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bi3.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bi3.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bi3_validation.pdf.gz | 459.5 KB | Display | wwPDB validaton report |
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Full document | 3bi3_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 3bi3_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3bi3_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3bi3 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3bi3 | HTTPS FTP |
-Related structure data
Related structure data | 3bieC 3bkzC 3btxC 3btyC 3btzC 3bu0C 3bucC 3bhz 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: 22314.504 Da / Num. of mol.: 1 / Fragment: catalytic repair domain / Mutation: S129C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: alkB, aidD / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P05050, 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: 4074.788 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, 170 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: 2.51 Å3/Da / Density % sol: 50.91 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% (w/v) PEG 8K, 100 mM Sodium Chloride, 25 mM magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 24645 / Num. obs: 24645 / % possible obs: 89.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / % possible all: 69.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.117 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.164 / 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: 32.669 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.5917 Å / Origin y: 1.7121 Å / Origin z: -23.2903 Å
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