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Yorodumi- PDB-4bbm: CRYSTAL STRUCTURE OF THE HUMAN CDKL2 KINASE DOMAIN WITH BOUND TCS 2312 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bbm | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN CDKL2 KINASE DOMAIN WITH BOUND TCS 2312 | ||||||
Components | CYCLIN-DEPENDENT KINASE-LIKE 2 | ||||||
Keywords | TRANSFERASE / PHOSPHO-MIMETIC | ||||||
Function / homology | Function and homology information sex differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / phosphorylation / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / nucleoplasm ...sex differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / phosphorylation / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Canning, P. / Elkins, J.M. / Cooper, C.D.O. / Mahajan, P. / Daga, N. / Berridge, G. / Burgess-Brown, N. / Muniz, J.R.C. / Krojer, T. / Arrowsmith, C.H. ...Canning, P. / Elkins, J.M. / Cooper, C.D.O. / Mahajan, P. / Daga, N. / Berridge, G. / Burgess-Brown, N. / Muniz, J.R.C. / Krojer, T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A. | ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function. Authors: Canning, P. / Park, K. / Goncalves, J. / Li, C. / Howard, C.J. / Sharpe, T.D. / Holt, L.J. / Pelletier, L. / Bullock, A.N. / Leroux, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bbm.cif.gz | 253.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bbm.ent.gz | 202.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bbm_validation.pdf.gz | 858.5 KB | Display | wwPDB validaton report |
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Full document | 4bbm_full_validation.pdf.gz | 867.8 KB | Display | |
Data in XML | 4bbm_validation.xml.gz | 25 KB | Display | |
Data in CIF | 4bbm_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/4bbm ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bbm | HTTPS FTP |
-Related structure data
Related structure data | 3zduC 4aaaSC 4aguC 4bgqC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: -3 - 308 / Label seq-ID: 20 - 331
NCS oper: (Code: given Matrix: (-1, 0.0014, 0.0052), Vector: |
-Components
#1: Protein | Mass: 38390.457 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-308 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: SITE-DIRECTED MUTAGENESIS / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q92772, cyclin-dependent kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Nonpolymer details | 4'-[5-[[3-[(CYCLOPROPYLAMINO)METHYL] PHENYL]AMINO]-1H-PYRAZOL-3-YL]-[1,1'-BIPHENYL]-2,4- DIOL (TC0): ...4'-[5-[[3-[(CYCLOPROPY | Sequence details | TWO PHOSPHO-MIMETIC ACTIVATING | |
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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: 2.19 Å3/Da / Density % sol: 43.85 % / Description: NONE |
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Crystal grow | Details: 0.2M (NH4)2SO4, 0.1M CACODYLATE PH 6.5, 30% PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.39 Å / Num. obs: 42854 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.4 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AAA Resolution: 2→39.39 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.301 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 28.105 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.39 Å
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Refine LS restraints |
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