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Yorodumi- PDB-3p1a: Structure of human Membrane-associated Tyrosine- and Threonine-sp... -
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-Basic information
Entry | Database: PDB / ID: 3p1a | ||||||
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Title | Structure of human Membrane-associated Tyrosine- and Threonine-specific cdc2-inhibitory kinase MYT1 (PKMYT1) | ||||||
Components | Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / Protein kinase / Tyrosine- and threonine-specific kinase / membrane-associated protein kinase | ||||||
Function / homology | Function and homology information negative regulation of G2/MI transition of meiotic cell cycle / G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / regulation of mitotic nuclear division / regulation of cyclin-dependent protein serine/threonine kinase activity / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity ...negative regulation of G2/MI transition of meiotic cell cycle / G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / regulation of mitotic nuclear division / regulation of cyclin-dependent protein serine/threonine kinase activity / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / nucleolus / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Chaikuad, A. / Eswaran, J. / Fedorov, O. / Cooper, C.D.O. / Kroeler, T. / Vollmar, M. / Krojer, T. / Berridge, G. / Muniz, J.R.C. / Pike, A.C.W. ...Chaikuad, A. / Eswaran, J. / Fedorov, O. / Cooper, C.D.O. / Kroeler, T. / Vollmar, M. / Krojer, T. / Berridge, G. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Structure of human Membrane-associated Tyrosine- and Threonine-specific cdc2-inhibitory kinase MYT1 (PKMYT1) Authors: Chaikuad, A. / Eswaran, J. / Fedorov, O. / Cooper, C.D.O. / Kroeler, T. / Vollmar, M. / Krojer, T. / Berridge, G. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C. ...Authors: Chaikuad, A. / Eswaran, J. / Fedorov, O. / Cooper, C.D.O. / Kroeler, T. / Vollmar, M. / Krojer, T. / Berridge, G. / Muniz, J.R.C. / Pike, A.C.W. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p1a.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p1a.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 3p1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p1a_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 3p1a_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 3p1a_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3p1a_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/3p1a ftp://data.pdbj.org/pub/pdb/validation_reports/p1/3p1a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34498.133 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residue 75-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYT1, PKMYT1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 References: UniProt: Q99640, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: 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: 2.12 Å3/Da / Density % sol: 42.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 3350, 0.2M KSCN, 0.1M Bis-Tris Propane, pH 6.5, 10% Ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9245 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2010 / Details: Kirkpatrick Baez bimorph mirror pair |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9245 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.32 Å / Num. all: 32606 / Num. obs: 32553 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4497 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2C30 and 3CR0 Resolution: 1.7→30.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.42 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.802 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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