+Open data
-Basic information
Entry | Database: PDB / ID: 5ca1 | ||||||
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Title | Crystal structure of T2R-TTL-Nocodazole complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Inhibitor / Complex / Tubulin | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / microtubule depolymerization / negative regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / microtubule depolymerization / negative regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / growth cone / microtubule / hydrolase activity / neuron projection / nucleotide binding / GTPase activity / calcium ion binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Rattus norvegicus (Norway rat) Sus barbatus (bearded pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Wang, Y. / Yu, Y. / Chen, Q. / Yang, J. | ||||||
Citation | Journal: Febs J. / Year: 2016 Title: Structures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery. Authors: Wang, Y. / Zhang, H. / Gigant, B. / Yu, Y. / Wu, Y. / Chen, X. / Lai, Q. / Yang, Z. / Chen, Q. / Yang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ca1.cif.gz | 460.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ca1.ent.gz | 366 KB | Display | PDB format |
PDBx/mmJSON format | 5ca1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/5ca1 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/5ca1 | HTTPS FTP |
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-Related structure data
Related structure data | 5c8yC 5ca0C 5cb4C 4i55S C: citing same article (ref.) 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: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I993*PLUS #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P32882 #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 49-189 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, 392 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-ACP / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1M MES, 30mM CaCl2, 30mM MgCl2, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 118147 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 12.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I55 Resolution: 2.401→41.523 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.61 / 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: 2.401→41.523 Å
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Refine LS restraints |
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LS refinement shell |
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