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Yorodumi- PDB-2vx3: Crystal structure of the human dual specificity tyrosine- phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vx3 | ||||||
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Title | Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A | ||||||
Components | DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MINIBRAIN HOMOLOG / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / TYROSINE-PROTEIN KINASE / CASP8 / KINASE | ||||||
Function / homology | Function and homology information histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation / negative regulation of DNA damage response, signal transduction by p53 class mediator / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / : / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / circadian rhythm / peptidyl-tyrosine phosphorylation / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Roos, A.K. / Soundararajan, M. / Pike, A.C.W. / Federov, O. / King, O. / Burgess-Brown, N. / Philips, C. / Filippakopoulos, P. / Arrowsmith, C.H. / Wikstrom, M. ...Roos, A.K. / Soundararajan, M. / Pike, A.C.W. / Federov, O. / King, O. / Burgess-Brown, N. / Philips, C. / Filippakopoulos, P. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A. / von Delft, F. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structures of Down Syndrome Kinases, Dyrks, Reveal Mechanisms of Kinase Activation and Substrate Recognition. Authors: Soundararajan, M. / Roos, A.K. / Savitsky, P. / Filippakopoulos, P. / Kettenbach, A.N. / Olsen, J.V. / Gerber, S.A. / Eswaran, J. / Knapp, S. / Elkins, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vx3.cif.gz | 297.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vx3.ent.gz | 240.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vx3_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 2vx3_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 2vx3_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 2vx3_validation.cif.gz | 70.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vx3 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vx3 | HTTPS FTP |
-Related structure data
Related structure data | 2wo6C 3k2lC 1exeS 1z57S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44553.188 Da / Num. of mol.: 4 / Fragment: RESIDUES 127-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q13627, dual-specificity kinase |
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-Non-polymers , 5 types, 233 molecules
#2: Chemical | ChemComp-D15 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-P6G / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PHOSPHOTYR |
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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: 3.02 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 34% PEG 300, 0.1 M LISO4, TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→26.35 Å / Num. obs: 92815 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EXE AND 1Z57 Resolution: 2.4→26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.127 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.208 / 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: 27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→26 Å
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Refine LS restraints |
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