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- PDB-5w80: Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-237 -

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Basic information

Entry
Database: PDB / ID: 5w80
TitleToxoplasma Gondii CDPK1 in complex with inhibitor GXJ-237
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / CDPK / PARASITOLOGY / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
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-9XJ / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-237
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. / ...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. / Structural Genomics Consortium (SGC)
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,6263
Polymers55,2271
Non-polymers3992
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.969, 72.815, 65.528
Angle α, β, γ (deg.)90.00, 99.53, 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-9XJ / 3-(3-chlorophenoxy)-1-[(piperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 358.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19ClN6O
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.04 Å3/Da / Density % sol: 39.83 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG8K, 0.2M NaCl, 0.1M Hepes pH7.5, 10 % Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 28, 2015 / Details: MARMOSAIC CCD300
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→48.33 Å / Num. obs: 30132 / Biso Wilson estimate: 30.5 Å2
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.050.460.9120.2590.5394.1
8.93-48.330.0390.9960.0230.04599.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.12data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4IH8

4ih8


Resolution: 2→48.33 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.931 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.193 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1485 4.93 %RANDOM
Rwork0.185 ---
obs0.188 30132 100 %-
Displacement parametersBiso mean: 41.72 Å2
Baniso -1Baniso -2Baniso -3
1-8.6048 Å20 Å23.5782 Å2
2---2.8542 Å20 Å2
3----5.7505 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 2→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 26 244 3778
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097205HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.813012HARMONIC2.8
X-RAY DIFFRACTIONt_dihedral_angle_d1618SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1117HARMONIC5
X-RAY DIFFRACTIONt_it7205HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion15.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
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_contact7967SEMIHARMONIC4
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.234 161 5.5 %
Rwork0.19 2764 -
all0.193 2925 -
obs--99.79 %
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)
12.4494-1.52921.36043.5854-1.28982.3486-0.1851-0.14920.01990.5373-0.0008-0.1314-0.33640.13830.1860.0103-0.0076-0.0081-0.0796-0.01390.0215-13.8193-15.5747104.5215
20.9073-0.23520.56851.5892-0.92641.36590.07450.1641-0.0647-0.1167-0.187-0.07780.18810.1610.1126-0.08860.02520.0186-0.019-0.0110.0229-15.6506-13.883385.7234
31.03310.00270.56021.53430.33791.13150.04340.2858-0.0518-0.0189-0.0142-0.14110.11990.182-0.0291-0.11220.04320.0336-0.03910.0159-0.078-8.9655-7.617783.4065
42.0688-1.38040.81474.8252-1.66022.62850.02630.0975-0.10970.21460.0105-0.11570.11270.0766-0.03690.065-0.0154-0.1419-0.08440.00160.05863.1525-5.3689113.2093
55.2709-0.5456-1.84611.06240.89143.36880.14450.11140.49640.06170.0978-0.0605-0.2014-0.0828-0.2423-0.11040.03280.0084-0.06720.04930.06625.95235.999885.3394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|43 - 99 }
2X-RAY DIFFRACTION2{ A|100 - 262 }
3X-RAY DIFFRACTION3{ A|263 - 380 }
4X-RAY DIFFRACTION4{ A|381 - 438 }
5X-RAY DIFFRACTION5{ A|439 - 507 }

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