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Yorodumi- PDB-1vzo: The structure of the N-terminal kinase domain of MSK1 reveals a n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vzo | ||||||
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Title | The structure of the N-terminal kinase domain of MSK1 reveals a novel autoinhibitory conformation for a dual kinase protein | ||||||
Components | RIBOSOMAL PROTEIN S6 KINASE ALPHA 5Ribosome | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / PHOSPHORYLATION / SERINE/THREONINE PROTEIN KINASE | ||||||
Function / homology | Function and homology information histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / regulation of postsynapse organization / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / Recycling pathway of L1 / ERK/MAPK targets ...histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / regulation of postsynapse organization / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / Recycling pathway of L1 / ERK/MAPK targets / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / post-translational protein modification / axon guidance / positive regulation of NF-kappaB transcription factor activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Smith, K.J. / Carter, P.S. / Bridges, A. / Horrocks, P. / Lewis, C. / Pettman, G. / Clarke, A. / Brown, M. / Hughes, J. / Wilkinson, M. ...Smith, K.J. / Carter, P.S. / Bridges, A. / Horrocks, P. / Lewis, C. / Pettman, G. / Clarke, A. / Brown, M. / Hughes, J. / Wilkinson, M. / Bax, B. / Reith, A. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The Structure of Msk1 Reveals a Novel Autoinhibitory Conformation for a Dual Kinase Protein Authors: Smith, K.J. / Carter, P.S. / Bridges, A. / Horrocks, P. / Lewis, C. / Pettman, G. / Clarke, A. / Brown, M. / Hughes, J. / Wilkinson, M. / Bax, B. / Reith, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vzo.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vzo.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vzo ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vzo | HTTPS FTP |
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-Related structure data
Related structure data | 1atpS 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
#1: Protein | Mass: 39914.375 Da / Num. of mol.: 1 / Fragment: N-TERMINAL KINASE DOMAIN, RESIDUES 1-350 / Mutation: YES Source method: isolated from a genetically manipulated source Details: A COVALENT B-MERCAPTOETHANOL ADDUCT INCLUDED ON CYSTINE A 304 Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: BACMID / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75582, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-BME / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Compound details | SERINE/THREONINE KINASE THAT MAY PLAY A ROLE IN MEDIATING THE GROWTH-FACTOR AND STRESS INDUCED ...SERINE/THREONINE KINASE THAT MAY PLAY A ROLE IN MEDIATING THE GROWTH-FACTOR AND STRESS INDUCED ACTIVATION |
Sequence details | SERINE 212 MUTATED TO ASPARTIC ACID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % Description: SOME DATA WERE EXCLUDED BECAUSE OF ICE-RINGS WHICH AFFECTED REFINEMENT |
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Crystal grow | pH: 9.5 / Details: 2.0M AMMONIUM SULPHATE, 0.1M TRIS PH8.5, pH 9.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 |
Detector | Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 34183 / % possible obs: 94.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ATP Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.01 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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