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Yorodumi- PDB-3feg: Crystal structure of human choline kinase beta in complex with ph... -
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-Basic information
Entry | Database: PDB / ID: 3feg | ||||||
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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 / Kinase / 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 / ATP binding ...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 / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.302 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 | 3feg.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3feg.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 3feg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/3feg ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3feg | HTTPS FTP |
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-Related structure data
Related structure data | 3g15C 3lq3C 2ig7S 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: 44002.613 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, 305 molecules
#2: Chemical | ChemComp-HC7 / ( | ||
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#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-ADP / | ||
#5: Chemical | ChemComp-AMP / | ||
#6: Chemical | ChemComp-MG / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | FOR THE LIGAND HC7 THE STEREO-CENTER AT THE "2" POSITION IS SPECIFIED AS (2S), HOWEVER CAN BE (2R) ...FOR THE LIGAND HC7 THE STEREO-CENTER AT THE "2" POSITION IS SPECIFIED AS (2S), HOWEVER CAN BE (2R) OR (2S) AS THE MORPHOLINI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: protein buffer: 0.01M Tris pH 8, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP; precipitant: 0.1M sodium cacodylate, 30% PEG-4000, 0.2M ...Details: protein buffer: 0.01M Tris pH 8, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP; precipitant: 0.1M sodium cacodylate, 30% PEG-4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97243 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 6, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97243 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→30 Å / Num. obs: 92472 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Χ2: 1.578 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ig7 Resolution: 1.302→28.296 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.162 / SU B: 1.51 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Hemicholinium restraints were calculated by the PRODRG server.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.302→28.296 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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