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Yorodumi- PDB-3bie: X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bie | ||||||
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Title | X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG | ||||||
Components |
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Keywords | Oxidoreductase/DNA / Dioxygenase / protein DNA interaction / cross-linking / alkylation repair / 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: 1.68 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 | 3bie.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bie.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3bie ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3bie | HTTPS FTP |
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-Related structure data
Related structure data | 3bi3C 3bkzC 3btxC 3btyC 3btzC 3bu0C 3bucC 2qxq 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: 22443.684 Da / Num. of mol.: 1 / Fragment: catalytic 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: 3770.595 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3941.584 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 261 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: 2.58 Å3/Da / Density % sol: 52.39 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24w/v% PEG 8000, 100mM sodium chloride, 50mM 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-D / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. all: 34683 / Num. obs: 34683 / % possible obs: 88.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.87 / Num. unique all: 2207 / % possible all: 56.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.75 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.103 / 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: 24.991 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.723 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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