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- PDB-4csv: Tyrosine kinase AS - a common ancestor of Src and Abl bound to Gleevec -

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Basic information

Entry
Database: PDB / ID: 4csv
TitleTyrosine kinase AS - a common ancestor of Src and Abl bound to Gleevec
ComponentsSRC-ABL TYROSINE KINASE ANCESTOR
KeywordsTRANSFERASE / DFG
Function / homologyPhosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / Chem-STI
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKutter, S. / Wilson, C. / Cruz, L. / Agafonov, R.V. / Hoemberger, M.S. / Zorba, A. / Kern, D.
CitationJournal: 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
DepositionMar 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SRC-ABL TYROSINE KINASE ANCESTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7502
Polymers31,2571
Non-polymers4941
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.029, 56.869, 76.118
Angle α, β, γ (deg.)90.00, 116.62, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein SRC-ABL TYROSINE KINASE ANCESTOR


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
#2: Chemical ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31N7O / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.42 % / Description: NONE
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999956
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2014
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999956 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.05→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
MOLREPAUTO MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CDS

4cds
PDB Unreleased entry


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
RfactorNum. reflection% reflectionSelection details
Rfree0.24159 886 5.9 %RANDOM
Rwork0.18728 ---
obs0.19044 14124 87.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å22.67 Å2
2---3.16 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.05→62.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 37 56 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192057
X-RAY DIFFRACTIONr_bond_other_d0.0020.021933
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9792785
X-RAY DIFFRACTIONr_angle_other_deg0.97434450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71924.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28615352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2241511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212301
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02483
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5855.659971
X-RAY DIFFRACTIONr_mcbond_other3.5715.655970
X-RAY DIFFRACTIONr_mcangle_it5.2078.4641209
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2196.221086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 54 -
Rwork0.305 1137 -
obs--91.33 %

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