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Yorodumi- PDB-2fdi: Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fdi | ||||||
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Title | Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T (air 3 hours) | ||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / beta jellyroll / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / 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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yu, B. / Benach, J. / Edstrom, W.C. / Gibney, B.R. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Nature / Year: 2006 Title: Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Authors: Yu, B. / Edstrom, W.C. / Benach, J. / Hamuro, Y. / Weber, P.C. / Gibney, B.R. / Hunt, J.F. | ||||||
History |
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Remark 600 | HETEROGEN The close contacts in remark 500 are due to iron coordination. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fdi.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fdi.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/2fdi ftp://data.pdbj.org/pub/pdb/validation_reports/fd/2fdi | HTTPS FTP |
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-Related structure data
Related structure data | 2fd8SC 2fdfC 2fdgC 2fdhC 2fdjC 2fdkC S: Starting model for refinement C: citing same article (ref.) |
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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
-DNA chain / Protein , 2 types, 2 molecules BA
#1: DNA chain | Mass: 891.669 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 23610.975 Da / Num. of mol.: 1 / Fragment: residues 12-216 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: pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05050 |
-Non-polymers , 4 types, 108 molecules
#3: Chemical | ChemComp-FE2 / |
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#4: Chemical | ChemComp-AKG / |
#5: Chemical | ChemComp-SIN / |
#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: 1.99 Å3/Da / Density % sol: 38.09 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 22-24% (w/v) PEG 3350, 10% glycerol and 200 mM sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2005 / Details: mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 17611 / % possible obs: 99.2 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.102 / Χ2: 1.104 / Net I/σ(I): 20.93 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.15 / Num. unique all: 1748 / Χ2: 0.892 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 2FD8 Resolution: 1.8→19.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 919070.312 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.428 Å2 / ksol: 0.401 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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