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Yorodumi- PDB-4jht: Crystal Structure of AlkB in complex with 5-carboxy-8-hydroxyquin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jht | ||||||
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Title | Crystal Structure of AlkB in complex with 5-carboxy-8-hydroxyquinoline (IOX1) | ||||||
Components | Alpha-ketoglutarate-dependent dioxygenase AlkB | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / double-stranded beta helix / jelly-roll motif / oxidoreductase / dioxygenase / Nucleic acid demethylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR 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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 1.18 Å | ||||||
Authors | Aik, W.S. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Chem Sci / Year: 2013 Title: 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation. Authors: Hopkinson, R.J. / Tumber, A. / Yapp, C. / Chowdhury, R. / Aik, W. / Che, K.H. / Li, X.S. / Kristensen, J.B.L. / King, O.N.F. / Chan, M.C. / Yeoh, K.K. / Choi, H. / Walport, L.J. / Thinnes, C. ...Authors: Hopkinson, R.J. / Tumber, A. / Yapp, C. / Chowdhury, R. / Aik, W. / Che, K.H. / Li, X.S. / Kristensen, J.B.L. / King, O.N.F. / Chan, M.C. / Yeoh, K.K. / Choi, H. / Walport, L.J. / Thinnes, C.C. / Bush, J.T. / Lejeune, C. / Rydzik, A.M. / Rose, N.R. / Bagg, E.A. / McDonough, M.A. / Krojer, T. / Yue, W.W. / Ng, S.S. / Olsen, L. / Brennan, P.E. / Oppermann, U. / Muller-Knapp, S. / Klose, R.J. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jht.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jht.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jht_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 4jht_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 4jht_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 4jht_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jht ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jht | HTTPS FTP |
-Related structure data
Related structure data | 4bioC 4bisC 3t4vS S: Starting model for refinement 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: 22945.236 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 12-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aidD, alkB, b2212, JW2200 / Plasmid details: PIR1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05050, DNA oxidative demethylase |
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-Non-polymers , 5 types, 273 molecules
#2: Chemical | ChemComp-8XQ / |
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#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-DMS / |
#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: 2.21 Å3/Da / Density % sol: 44.37 % / Mosaicity: 0.508 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23% PEG 3350, 0.264M NaCl, 0.1M HEPES pH7.5, 1mM 8XQ, 1mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.18→50 Å / Num. all: 64400 / Num. obs: 60068 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.036 / Net I/σ(I): 17.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: Isomorphous Replacement Starting model: PDB ID 3T4V Resolution: 1.18→38.77 Å / Occupancy max: 1 / Occupancy min: 0.3
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Displacement parameters | Biso max: 56.85 Å2 / Biso mean: 21.6921 Å2 / Biso min: 9.29 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→38.77 Å
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Refine LS restraints |
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LS refinement shell |
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