+Open data
-Basic information
Entry | Database: PDB / ID: 5xhc | ||||||
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Title | Crystal structure of T2R-TTL-PO10 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / TUBULIN / MICROTUBULE / COLCHICINE / STATHMIN | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle ...tubulin-tyrosine ligase activity / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / growth cone / microtubule / hydrolase activity / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Sus barbatus (bearded pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Chu, Y. / Wang, Y. / Yang, J. / Li, W. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Synthesis, biological evaluation and X-ray structure of anti-microtubule agents Authors: Chu, Y. / Wang, Y. / Yang, J. / Li, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhc.cif.gz | 451.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhc.ent.gz | 358.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xhc_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5xhc_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5xhc_validation.xml.gz | 72.5 KB | Display | |
Data in CIF | 5xhc_validation.cif.gz | 99 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhc ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhc | HTTPS FTP |
-Related structure data
Related structure data | 5xi5C 5xi7C 5fnvS 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 , 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 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I995 #3: Protein | | Mass: 21637.688 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 6-189 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 , 8 types, 118 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-GDP / | #9: Chemical | #10: Chemical | ChemComp-87U / ( | #11: Chemical | ChemComp-ACP / | #12: 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: 3.12 Å3/Da / Density % sol: 60.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→119.38 Å / Num. obs: 78443 / % possible obs: 99.8 % / Redundancy: 4.2 % / Net I/σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FNV Resolution: 2.75→119.38 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.866 / SU B: 15.821 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R: 1.242 / ESU R Free: 0.377 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.487 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→119.38 Å
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Refine LS restraints |
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