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- PDB-4ihp: Crystal structure of TgCDPK1 with inhibitor bound -

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Basic information

Entry
Database: PDB / ID: 4ihp
TitleCrystal structure of TgCDPK1 with inhibitor bound
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / Structural Genomics Consortium / SGC / Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane
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 ...: / 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-1FB / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsEl Bakkouri, M. / Tempel, W. / Crandall, I.E. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, C.K. ...El Bakkouri, M. / Tempel, W. / Crandall, I.E. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, C.K. / Shokat, K.M. / Sibley, L.D. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of TgCDPK1 with inhibitor bound
Authors: El Bakkouri, M. / Tempel, W. / Crandall, I.E. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, C.K. / Shokat, K.M. / Sibley, L.D. / Hui, R. ...Authors: El Bakkouri, M. / Tempel, W. / Crandall, I.E. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, C.K. / Shokat, K.M. / Sibley, L.D. / Hui, R. / Structural Genomics Consortium (SGC)
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6514
Polymers57,3331
Non-polymers3183
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.309, 73.235, 149.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin-domain protein kinase 1 / Calmodulin-domain protein kinase / putative


Mass: 57333.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TGGT1_059880, TGVEG_042030 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-1FB / 1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 317.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16ClN5O
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG3350, 0.2M K OAc, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97932 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionHighest resolution: 2.27 Å / Num. obs: 25233 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 46.876 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.27-2.410.8052.6628149388696.8
2.41-2.570.553.97280183777100
2.57-2.770.3496.01259233495100
2.77-3.040.1910.72243323290100
3.04-3.390.10518.17217312953100
3.39-3.910.06228.78190422635100
3.91-4.760.04240.21160352265100
4.76-6.650.04140.28125831814100
6.650.0347.687099111898

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2229 / WRfactor Rwork: 0.1737 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.845 / SU B: 6.738 / SU ML: 0.164 / SU R Cruickshank DPI: 0.2869 / SU Rfree: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1279 5.1 %RANDOM
Rwork0.1921 ---
obs0.195 25174 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.81 Å2 / Biso mean: 45.3645 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.96 Å2-0 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 24 89 3666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193712
X-RAY DIFFRACTIONr_bond_other_d0.0010.023535
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9745015
X-RAY DIFFRACTIONr_angle_other_deg0.7663.0028141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72824.518166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62815685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.071522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
X-RAY DIFFRACTIONr_mcbond_it2.9164.3851844
X-RAY DIFFRACTIONr_mcbond_other2.9164.3841843
X-RAY DIFFRACTIONr_mcangle_it4.336.5582308
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 95 -
Rwork0.275 1670 -
all-1765 -
obs--96.29 %

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