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Yorodumi- PDB-3o1p: Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o1p | ||||||
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Title | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Demethylase | ||||||
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: 1.51 Å | ||||||
Authors | Yi, C. / Jia, G. / Hou, G. / Dai, Q. / Zhang, W. / Zheng, G. / Jian, X. / Yang, C.-G. / Cui, Q. / He, C. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Authors: Yi, C. / Jia, G. / Hou, G. / Dai, Q. / Zhang, W. / Zheng, G. / Jian, X. / Yang, C.G. / Cui, Q. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o1p.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o1p.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 3o1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/3o1p ftp://data.pdbj.org/pub/pdb/validation_reports/o1/3o1p | HTTPS FTP |
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-Related structure data
Related structure data | 3o1mC 3o1oC 3o1rC 3o1sC 3o1tC 3o1uC 3o1vC 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: 22961.303 Da / Num. of mol.: 1 Fragment: N-terminus 11 amino acid truncated AlkB (UNP residues 12 to 216) 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) / Strain (production host): D3-157 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: 4083.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid-state DNA synthesizer. |
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#3: DNA chain | Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid-state DNA synthesizer. |
-Non-polymers , 4 types, 350 molecules
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-AKG / |
#6: Chemical | ChemComp-GOL / |
#7: 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: 2.49 Å3/Da / Density % sol: 50.53 % |
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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 |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9266 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9266 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. all: 43144 / Num. obs: 41850 / % possible obs: 97 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 3.4 % / Rmerge(I) obs: 0.341 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.51→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BIE Resolution: 1.51→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.678 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 2.2 / σ(I): 2.2 / ESU R Free: 0.084 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 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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