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Yorodumi- PDB-2buj: Crystal structure of the human Serine-threonine Kinase 16 in comp... -
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-Basic information
Entry | Database: PDB / ID: 2buj | ||||||
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Title | Crystal structure of the human Serine-threonine Kinase 16 in complex with staurosporine | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE 16Serine/threonine-specific protein kinase | ||||||
Keywords | TRANSFERASE / ATP-BINDING / KINASE / LIPOPROTEIN / MYRISTATE / PALMITATE / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | Function and homology information Golgi-associated vesicle / cellular response to transforming growth factor beta stimulus / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein serine/threonine kinase activity / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II ...Golgi-associated vesicle / cellular response to transforming growth factor beta stimulus / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein serine/threonine kinase activity / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Debreczeni, J.E. / Eswaran, J. / Bullock, A. / Filippakopoulos, P. / Kavanagh, K. / Amos, A. / Fedorov, O. / Sobott, F. / Ball, L.J. / von Delft, F. ...Debreczeni, J.E. / Eswaran, J. / Bullock, A. / Filippakopoulos, P. / Kavanagh, K. / Amos, A. / Fedorov, O. / Sobott, F. / Ball, L.J. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Human Serine-Threonine Kinase 16 in Complex with Staurosporine Authors: Debreczeni, J.E. / Eswaran, J. / Bullock, A. / Filippakopoulos, P. / Kavanagh, K. / Amos, A. / Fedorov, O. / Sobott, F. / Ball, L.J. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2buj.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2buj.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 2buj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/2buj ftp://data.pdbj.org/pub/pdb/validation_reports/bu/2buj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.77547, 0.63133, 0.00832), Vector: |
-Components
#1: Protein | Mass: 36306.488 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P11-TORONTO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA II / References: UniProt: O75716, EC: 2.7.1.37 #2: Chemical | #3: Chemical | ChemComp-STU / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 18 TO HIS ENGINEERED RESIDUE IN CHAIN B, ARG 18 TO HIS ...ENGINEERED | Sequence details | MUTATION R18H AND R265W | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.3 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: 200 NL SITTING DROP, 1.1 AMMONIUM SULFATE, 1% PEG3350, 0.1 M BIS-TRIS PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 23, 2005 / Details: MIRRORS |
Radiation | Monochromator: SILICON MONOCHROMATORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→64.8 Å / Num. obs: 35446 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.83 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.52 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 5.12 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.29 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→64.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.62 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.228 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→64.82 Å
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Refine LS restraints |
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