+Open data
-Basic information
Entry | Database: PDB / ID: 5ov7 | ||||||
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Title | tubulin - rigosertib complex | ||||||
Components |
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Keywords | CELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | ||||||
Authors | Menchon, G. / Prota, A.E. / Steinmetz, M. / Jost, M. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent. Authors: Jost, M. / Chen, Y. / Gilbert, L.A. / Horlbeck, M.A. / Krenning, L. / Menchon, G. / Rai, A. / Cho, M.Y. / Stern, J.J. / Prota, A.E. / Kampmann, M. / Akhmanova, A. / Steinmetz, M.O. / ...Authors: Jost, M. / Chen, Y. / Gilbert, L.A. / Horlbeck, M.A. / Krenning, L. / Menchon, G. / Rai, A. / Cho, M.Y. / Stern, J.J. / Prota, A.E. / Kampmann, M. / Akhmanova, A. / Steinmetz, M.O. / Tanenbaum, M.E. / Weissman, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ov7.cif.gz | 912.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ov7.ent.gz | 752.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ov7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/5ov7 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ov7 | HTTPS FTP |
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-Related structure data
Related structure data | 4i4tS 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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Unit cell |
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-Components
-Protein , 4 types, 6 molecules ACBDEF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043 #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43 |
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-Non-polymers , 9 types, 364 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-MES / | #12: Chemical | ChemComp-ACP / | #13: Water | ChemComp-HOH / | |
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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: 2.87 Å3/Da / Density % sol: 57.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 4 to 10% PEG 4K, 4 to 6% glycerol, 30 mM MgCl2, 30 mM CaCl2, and 100 mM MES/imidazole, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.1 Å / Num. obs: 116426 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.149 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 2.12 / Rrim(I) all: 2.229 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4i4t Resolution: 2.402→48.079 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→48.079 Å
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LS refinement shell |
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