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- PDB-5t6a: Crystal Structure of TgCDPK1 from toxoplasma gondii complexed with 5GA -

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Basic information

Entry
Database: PDB / ID: 5t6a
TitleCrystal Structure of TgCDPK1 from toxoplasma gondii complexed with 5GA
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / CDPKs / Serine/Threonine Protein Kinase / Nucleotide-Binding
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-5GA / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / Walker, J.R. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. ...Jiang, D.Q. / Tempel, W. / Loppnau, P. / Walker, J.R. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Osman, K.T. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of TgCDPK1 from toxoplasma gondii complexed with SGC-1-9
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Walker, J.R. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Osman, K.T. / Structural Genomics Consortium (SGC)
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionNov 2, 2016ID: 5DVU
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)59,8902
Polymers59,5331
Non-polymers3571
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.757, 72.175, 66.142
Angle α, β, γ (deg.)90.00, 97.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 59533.410 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(DE3) / References: UniProt: Q9BJF5
#2: Chemical ChemComp-5GA / 4-(3-chloro-4-fluorophenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine


Mass: 356.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H10ClFN4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, di Sodium-Tart

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.05→72.18 Å / Num. obs: 27510 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.74 Å2 / Net I/σ(I): 0.05

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
Aimless0.5.15data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3KU2

3ku2


Resolution: 2.05→25.55 Å / Cor.coef. Fo:Fc: 0.9481 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.712 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.202 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1360 4.95 %RANDOM
Rwork0.2026 ---
obs0.2045 27482 97.98 %-
Displacement parametersBiso mean: 65.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.8081 Å20 Å22.6116 Å2
2--2.1226 Å20 Å2
3----7.9306 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å
Refinement stepCycle: LAST / Resolution: 2.05→25.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 24 94 3429
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096537HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9211752HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1426SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1026HARMONIC5
X-RAY DIFFRACTIONt_it6537HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion15.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion457SEMIHARMONIC5
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_contact6918SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.13 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2481 139 5.02 %
Rwork0.2284 2629 -
all0.2294 2768 -
obs--93.73 %
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)
12.9319-0.02590.3012.82341.13911.5908-0.0373-0.01840.09540.10660.007-0.0513-0.07230.060.0304-0.0849-0.0508-0.0634-0.12010.10710.11033.6888-9.669341.4893
21.81590.29760.35162.5425-2.15333.0118-0.0918-0.0506-0.26360.0637-0.1073-0.16160.15650.12030.1991-0.18440.02030.0253-0.2120.03370.1013-4.0605-7.928626.58
31.76640.19120.60121.5073-0.48062.0282-0.15090.3544-0.1266-0.33490.0240.05920.17390.19420.127-0.15190.04140.0509-0.0971-0.007-0.0562-1.17651.765513.8127
42.3949-1.9638-0.46620-2.04062.50960.06320.0738-0.03610.1514-0.06830.0011-0.07520.03520.00510.2277-0.1467-0.0227-0.1753-0.0284-0.135519.80696.312951.4155
56.4015-2.1664-1.61594.59431.30834.23270.07980.00130.1760.01970.10780.158-0.3626-0.1925-0.1876-0.16050.0464-0.0075-0.07610.0858-0.022118.096415.533421.8505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|45 - 75}
2X-RAY DIFFRACTION2{A|76 - 213}
3X-RAY DIFFRACTION3{A|214 - 364}
4X-RAY DIFFRACTION4{A|365 - 440}
5X-RAY DIFFRACTION5{A|441 - 507}

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