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Yorodumi- PDB-3zm9: The mechanism of allosteric coupling in choline kinase a1 reveale... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zm9 | ||||||
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Title | The mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor | ||||||
Components | CHOLINE KINASE ALPHA | ||||||
Keywords | TRANSFERASE / NEGATIVE COOPERATIVITY / ALLOSTERIC MECHANISM / ELASTIC NETWORK ANALYSIS | ||||||
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 / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / phosphorylation / protein homodimerization activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sahun-Roncero, M. / Rubio-Ruiz, B. / Saladino, G. / Conejo-Garcia, A. / Espinosa, A. / Velazquez-Campoy, A. / Gervasio, F.L. / Entrena, A. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: The Mechanism of Allosteric Coupling in Choline Kinase A1 Revealed by a Rationally Designed Inhibitor Authors: Sahun-Roncero, M. / Rubio-Ruiz, B. / Saladino, G. / Conejo-Garcia, A. / Espinosa, A. / Velazquez-Campoy, A. / Gervasio, F.L. / Entrena, A. / Hurtado-Guerrero, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zm9.cif.gz | 304.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zm9.ent.gz | 247.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zm9 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zm9 | HTTPS FTP |
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-Related structure data
Related structure data | 3g15S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.2499, 0.8541, -0.4562), Vector: |
-Components
#1: Protein | Mass: 44954.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 75-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: P35790, choline kinase, ethanolamine kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 73 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 69213 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G15 Resolution: 1.9→131.86 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.576 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.097 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→131.86 Å
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Refine LS restraints |
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