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- PDB-5w8r: Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI -

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Basic information

Entry
Database: PDB / ID: 5w8r
TitleToxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI
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-9XV / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Toxoplasma Gondii CDPK1 in complex with inhibitor 3CIB-PPI
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 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 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)55,5833
Polymers55,2271
Non-polymers3562
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.024, 72.944, 65.546
Angle α, β, γ (deg.)90.00, 99.30, 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-9XV / 1-tert-butyl-3-[(3-chlorophenyl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 315.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18ClN5
#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.: 140 / 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: 2.05 Å3/Da / Density % sol: 40.06 % / Mosaicity: 0.598 °
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: 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: 2.2→48.4 Å / Num. obs: 22522 / Biso Wilson estimate: 42.21 Å2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.30.43510280.7940.2740.5170.81990.7
2.24-2.283.40.44210800.8450.2690.521.07593.8
2.28-2.323.60.39410770.9070.2360.460.67997.2
2.32-2.373.70.36511230.910.2160.4260.70899.4
2.37-2.423.90.33111320.9360.1910.3830.72199.7
2.42-2.484.10.32811120.9430.1840.3760.683100
2.48-2.544.10.29911490.9490.1660.3430.721100
2.54-2.614.20.25611230.9630.140.2920.733100
2.61-2.694.20.22711400.8620.1280.2620.906100
2.69-2.774.20.17711280.9810.0970.2020.785100
2.77-2.874.20.13911360.9870.0760.1590.815100
2.87-2.994.20.10911420.9930.060.1250.836100
2.99-3.124.20.09211240.9930.0510.1050.923100
3.12-3.294.20.0711270.9940.0390.080.954100
3.29-3.494.20.06211620.9960.0340.0711.135100
3.49-3.764.20.05511300.9960.0310.0641.32100
3.76-4.144.20.05611430.9940.0320.0651.898100
4.14-4.744.10.04711440.9960.0270.0541.841100
4.74-5.9740.0411560.9950.0230.0462.862100
5.97-5040.04311830.9920.0250.0512.05699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFG

4ifg


Resolution: 2.2→48.4 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.22
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1096 4.87 %RANDOM
Rwork0.2 ---
obs0.203 22522 98.8 %-
Displacement parametersBiso mean: 53.32 Å2
Baniso -1Baniso -2Baniso -3
1-7.7687 Å20 Å25.8846 Å2
2--3.3283 Å20 Å2
3----11.0971 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.2→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 23 140 3705
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087122HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7312832HARMONIC2.9
X-RAY DIFFRACTIONt_dihedral_angle_d1592SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1092HARMONIC5
X-RAY DIFFRACTIONt_it7122HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion15.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion484SEMIHARMONIC5
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_contact7694SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.241 124 4.49 %
Rwork0.198 2635 -
all0.2 2759 -
obs--91.52 %
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)
11.2972-0.62870.59982.7309-0.80322.7297-0.0622-0.1599-0.00850.3353-0.038-0.1333-0.12590.03130.1002-0.1108-0.0087-0.0211-0.134-0.0099-0.024-14.8568-17.4787102.0444
21.45730.29860.65161.535-0.5622.3920.06350.3219-0.0948-0.1232-0.1095-0.12230.32760.32510.0459-0.13870.04240.0119-0.0551-0.00430.0134-13.2388-16.124884.6245
31.18580.08420.74311.66320.38951.25280.01060.3057-0.0125-0.0332-0.0389-0.05080.17140.19140.0283-0.20410.04130.028-0.10210.0053-0.1477-10.7984-6.873282.8555
43.55680.9875-0.8043.92-1.34022.78760.07620.0017-0.09710.0734-0.0299-0.12250.12770.0728-0.04630.06280.0253-0.1987-0.11490.00760.0113.3539-5.4195113.1665
56.6399-0.7957-2.30891.32891.694.45140.15990.1340.51680.03020.1283-0.1531-0.209-0.1346-0.2882-0.1760.0331-0.012-0.12280.06380.03525.94795.597185.7957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|44 - 136 }
2X-RAY DIFFRACTION2{ A|137 - 214 }
3X-RAY DIFFRACTION3{ A|215 - 383 }
4X-RAY DIFFRACTION4{ A|384 - 438 }
5X-RAY DIFFRACTION5{ A|439 - 507 }

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