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Yorodumi- PDB-2zmc: Crystal structure of human mitotic checkpoint kinase Mps1 catalyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zmc | ||||||
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Title | Crystal structure of human mitotic checkpoint kinase Mps1 catalytic domain apo form | ||||||
Components | Dual specificity protein kinase TTK | ||||||
Keywords | TRANSFERASE / Kinase / Mps1 / mitosis / ATP-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å | ||||||
Authors | Chu, M.L.H. / Chavas, L.M.G. / Douglas, K.T. / Eyers, P.A. / Tabernero, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structure of the catalytic domain of the mitotic checkpoint kinase Mps1 in complex with SP600125. Authors: Chu, M.L. / Chavas, L.M. / Douglas, K.T. / Eyers, P.A. / Tabernero, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zmc.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zmc.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zmc_validation.pdf.gz | 731.3 KB | Display | wwPDB validaton report |
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Full document | 2zmc_full_validation.pdf.gz | 734.4 KB | Display | |
Data in XML | 2zmc_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 2zmc_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/2zmc ftp://data.pdbj.org/pub/pdb/validation_reports/zm/2zmc | HTTPS FTP |
-Related structure data
Related structure data | 2zmdC 1phkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44348.391 Da / Num. of mol.: 1 / Fragment: UNP residues 510-857, Catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1L1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P33981, dual-specificity kinase |
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#2: Chemical | ChemComp-7PE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG300, HEPES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→59.44 Å / Num. obs: 7029 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 84.992 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.056 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 3.14→3.31 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1030 / Rsym value: 0.283 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHK Resolution: 3.14→59.4 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.844 / SU B: 28.802 / SU ML: 0.462 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.85 Å2
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Refinement step | Cycle: LAST / Resolution: 3.14→59.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.14→3.222 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -44.5433 Å / Origin y: -22.6101 Å / Origin z: -13.5009 Å
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