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- PDB-5w9e: Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186 -

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Basic information

Entry
Database: PDB / ID: 5w9e
TitleToxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186
ComponentsCalmodulin-domain protein kinase 1
Keywordstransferase/transferase inhibitor / CDPK / PARASITOLOGY / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / transferase-transferase inhibitor complex
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9YJ / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å
AuthorsEl Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. ...El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R.
CitationJournal: To be published
Title: Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186
Authors: El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R.
History
DepositionJun 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5612
Polymers55,2271
Non-polymers3341
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.997, 72.802, 64.595
Angle α, β, γ (deg.)90.00, 98.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 55226.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Plasmid: PET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9BJF5
#2: Chemical ChemComp-9YJ / 1-tert-butyl-3-[(3-chlorophenyl)sulfanyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 333.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16ClN5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.02 Å3/Da / Density % sol: 39.15 % / Mosaicity: 0.53 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG8K, 0.2M NaCl, 0.1M Hepes pH7.5, 5 % Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.44→48.01 Å / Num. obs: 16313 / Biso Wilson estimate: 56.93 Å2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.44-2.541.0560.4760.6561.24788.3
8.79-48.010.0210.9990.0130.02599.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data collection
Aimless0.5.12data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.44→48.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.637 / SU Rfree Blow DPI: 0.278
RfactorNum. reflection% reflectionSelection details
Rfree0.249 781 4.79 %RANDOM
Rwork0.211 ---
obs0.213 16313 98.9 %-
Displacement parametersBiso mean: 62.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.1304 Å20 Å211.6165 Å2
2--3.9187 Å20 Å2
3----7.049 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.44→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 22 70 3574
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086937HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.6812504HARMONIC2.9
X-RAY DIFFRACTIONt_dihedral_angle_d1543SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1065HARMONIC5
X-RAY DIFFRACTIONt_it6937HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion15.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion477SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7085SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.241 128 4.56 %
Rwork0.225 2678 -
all0.225 2806 -
obs--94.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9111-0.27781.04942.4867-1.26073.94780.0189-0.02480.0860.0782-0.1926-0.20850.18770.19090.1736-0.1660.0151-0.0064-0.2020.0048-0.0352-12.7823-17.955593.9604
21.52030.14710.38322.6643-0.99872.6980.03680.09-0.0102-0.1746-0.16460.0180.1970.26670.1278-0.14360.03130.0054-0.0787-0.0073-0.0755-14.8658-7.174180.6892
31.01930.1030.97681.5328-0.10282.2381-0.04360.2316-0.0783-0.1152-0.0703-0.12170.26130.2210.1139-0.21260.1010.0473-0.13140.0107-0.1558-6.1534-7.815284.3054
42.04430.2034-0.77383.2229-1.25630.8690.01140.1339-0.04480.0344-0.0762-0.00630.0720.05950.06490.08570.066-0.1567-0.06060.0301-0.00555.1928-5.138110.716
57.3305-1.763-1.53171.06671.60854.57410.05010.08960.18050.0210.1114-0.0554-0.2264-0.066-0.1615-0.14230.0204-0.0236-0.11570.1011-0.00467.21436.126383.7508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|44 - 182 }
2X-RAY DIFFRACTION2{ A|183 - 266 }
3X-RAY DIFFRACTION3{ A|267 - 383 }
4X-RAY DIFFRACTION4{ A|384 - 441 }
5X-RAY DIFFRACTION5{ A|442 - 507 }

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