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Yorodumi- PDB-3lq3: Crystal structure of human choline kinase beta in complex with ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lq3 | ||||||
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Title | Crystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide | ||||||
Components | Choline/ethanolamine kinase | ||||||
Keywords | TRANSFERASE / NON-PROTEIN KINASE / CHOLINE KINASE / STRUCTURAL GENOMICS Consortium / SGC / hemicholinium-3 / phosphorylation / ATP-binding / Kinase / Nucleotide-binding / Phospholipid biosynthesis / Phosphoprotein | ||||||
Function / homology | Function and homology information ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / muscle organ development / Synthesis of PC / phosphorylation ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / muscle organ development / Synthesis of PC / phosphorylation / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å | ||||||
Authors | Hong, B.S. / Tempel, W. / Rabeh, W.M. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structures of human choline kinase isoforms in complex with hemicholinium-3: single amino acid near the active site influences inhibitor sensitivity. Authors: Hong, B.S. / Allali-Hassani, A. / Tempel, W. / Finerty, P.J. / Mackenzie, F. / Dimov, S. / Vedadi, M. / Park, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lq3.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lq3.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lq3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3lq3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3lq3_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3lq3_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/3lq3 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/3lq3 | HTTPS FTP |
-Related structure data
Related structure data | 3fegSC 3g15C 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: 46265.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHKB, CHETK, CHKL / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Y259, choline kinase, ethanolamine kinase |
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-Non-polymers , 7 types, 280 molecules
#2: Chemical | ChemComp-HC7 / ( | ||||||||
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#3: Chemical | ChemComp-MG / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-ADP / | #7: Chemical | ChemComp-AMP / | #8: 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: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 0.1M sodium cacodylate, 30% PEG4000, 0.2M ammonium sulfate. Protein buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M dtt. Ligands: 0.003M hemicholinium-3, 0. ...Details: 0.1M sodium cacodylate, 30% PEG4000, 0.2M ammonium sulfate. Protein buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M dtt. Ligands: 0.003M hemicholinium-3, 0.005M atp., vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC Q315 / Detector: CCD / Date: Nov 5, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→40 Å / Num. obs: 73581 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Χ2: 1.276 / Net I/σ(I): 10.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: direct placement of protein coordinates of pdb entry 3FEG Resolution: 1.42→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.186 / SU B: 1.095 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The program coot, as well as the PRODRG and MOLPROBITY servers were also used during refinement.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.708 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→30 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: 20
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