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Yorodumi- PDB-4csv: Tyrosine kinase AS - a common ancestor of Src and Abl bound to Gleevec -
+Open data
-Basic information
Entry | Database: PDB / ID: 4csv | ||||||
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Title | Tyrosine kinase AS - a common ancestor of Src and Abl bound to Gleevec | ||||||
Components | SRC-ABL TYROSINE KINASE ANCESTOR | ||||||
Keywords | TRANSFERASE / DFG | ||||||
Function / homology | Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / Chem-STI Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kutter, S. / Wilson, C. / Cruz, L. / Agafonov, R.V. / Hoemberger, M.S. / Zorba, A. / Kern, D. | ||||||
Citation | Journal: Science / Year: 2015 Title: Kinase Dynamics. Using Ancient Protein Kinases to Unravel a Modern Cancer Drug'S Mechanism. Authors: Wilson, C. / Agafonov, R.V. / Hoemberger, M. / Kutter, S. / Zorba, A. / Halpin, J. / Buosi, V. / Otten, R. / Waterman, D. / Theobald, D.L. / Kern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4csv.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4csv.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 4csv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4csv_validation.pdf.gz | 656.2 KB | Display | wwPDB validaton report |
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Full document | 4csv_full_validation.pdf.gz | 659.4 KB | Display | |
Data in XML | 4csv_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4csv_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4csv ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4csv | HTTPS FTP |
-Related structure data
Related structure data | 4ueuC 4cds 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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Unit cell |
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-Components
#1: Protein | Mass: 31256.531 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PETM-41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-STI / |
#3: 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: 2.17 Å3/Da / Density % sol: 43.42 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10 MG/ML OF LYSINE MODIFIED (ETHYLATED) PROTEIN IN 30 MM TRIS PH 8.0, 500 MM NACL, 1 MM GLEEVEC, MIXED 1:1 WITH 200 MM AMMONIUM ACETATE, 100 MM SODIUM ACETATE TRIHYDRATE PH 4.6 AND 30% PEG ...Details: 10 MG/ML OF LYSINE MODIFIED (ETHYLATED) PROTEIN IN 30 MM TRIS PH 8.0, 500 MM NACL, 1 MM GLEEVEC, MIXED 1:1 WITH 200 MM AMMONIUM ACETATE, 100 MM SODIUM ACETATE TRIHYDRATE PH 4.6 AND 30% PEG 4000, HANGING DROP, MICRO SEEDING WITH INITIAL CRYSTALS FROM A 96 WELL PLATE SCREEN, INITIAL CRYSTALS GREW ON A DUST PARTICLE, 18C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999956 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2014 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999956 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→42.36 Å / Num. obs: 15954 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CDS 4cds Resolution: 2.05→62.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.623 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 59.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→62.43 Å
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Refine LS restraints |
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