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Yorodumi- PDB-4zhn: Crystal Structure of AlkB T208A mutant protein in complex with Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zhn | ||||||
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Title | Crystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T | ||||||
Components |
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Keywords | Oxidoreductase/DNA / beta jellyroll / oxidoreductase-DNA complex / DNA repair enzyme / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.333 Å | ||||||
Authors | Ergel, B. / Yu, B. / Vorobiev, S.M. / Forouhar, F. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: DFT Studies of the Rate-Limiting Step in the Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related Experimental Studies Authors: Hall, M.L. / Ergel, B. / Miller, E.B. / Yu, B. / Rinaldo, D. / Hunt, J.F. / Friesner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zhn.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zhn.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4zhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zhn ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zhn | HTTPS FTP |
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-Related structure data
Related structure data | 2fd8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 891.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Protein | Mass: 23580.949 Da / Num. of mol.: 1 / Fragment: residues 12-216 / Mutation: T208A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: alkB, aidD, b2212, JW2200 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05050, DNA oxidative demethylase |
#3: Chemical | ChemComp-CO / |
#4: Chemical | ChemComp-AKG / |
#5: 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: 2.04 Å3/Da / Density % sol: 39.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 22-24% (w/v) PEG3350, 10% glycerol, 200 mM sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.33→30 Å / Num. obs: 44362 / % possible obs: 98.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 8.92 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.023 / Rrim(I) all: 0.053 / Χ2: 1.128 / Net I/av σ(I): 33.438 / Net I/σ(I): 17.4 / Num. measured all: 246733 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FD8 Resolution: 1.333→29.255 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 12.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.71 Å2 / Biso mean: 14.3926 Å2 / Biso min: 5.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.333→29.255 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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