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- PDB-5jn2: Crystal structure of TgCDPK1 bound to NVPACU106 -

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Basic information

Entry
Database: PDB / ID: 5jn2
TitleCrystal structure of TgCDPK1 bound to NVPACU106
ComponentsCalmodulin-domain protein kinase 1
KeywordsHYDROLASE / Kinase / 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-6LO / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEl Bakkouri, M. / Walker, J.R. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Lovato, D.V. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of TgCDPK1 bound to NVPACU106
Authors: El Bakkouri, M. / Walker, J.R. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Lovato, D.V. / Structural Genomics Consortium (SGC)
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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)60,0774
Polymers59,5331
Non-polymers5443
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.142, 72.473, 65.101
Angle α, β, γ (deg.)90.000, 98.630, 90.000
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BJF5
#2: Chemical ChemComp-6LO / N-[(3-{4-amino-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}cyclobutyl)methyl]acetamide


Mass: 441.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N5O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.96 Å3/Da / Density % sol: 37.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 8000, 0.2 M NaCl, 0.1 M Hepes pH7.5, 15 % Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97915 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22622 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 57.35 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Χ2: 1.436 / Net I/av σ(I): 38.653 / Net I/σ(I): 14.3 / Num. measured all: 95997
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.244.20.6981100
2.24-2.284.20.6481100
2.28-2.324.30.5021100
2.32-2.374.20.4051100
2.37-2.424.20.3281100
2.42-2.484.30.2991100
2.48-2.544.20.2371100
2.54-2.614.30.2151100
2.61-2.694.20.1671100
2.69-2.774.30.1381100
2.77-2.874.30.1131100
2.87-2.994.30.0941100
2.99-3.124.30.0741100
3.12-3.294.30.0541100
3.29-3.494.30.0411100
3.49-3.764.30.038199.9
3.76-4.144.30.047199.9
4.14-4.744.20.037199.9
4.74-5.974.20.0271100
5.97-504.10.024197.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
BUSTER2.10.2refinement
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IH8

4ih8


Resolution: 2.2→48.12 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.225
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 1096 4.86 %RANDOM
Rwork0.2328 ---
obs0.2347 22558 99.87 %-
Displacement parametersBiso max: 172.07 Å2 / Biso mean: 73.72 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-5.827 Å20 Å25.6859 Å2
2--2.4692 Å20 Å2
3----8.2962 Å2
Refine analyzeLuzzati coordinate error obs: 0.342 Å
Refinement stepCycle: final / Resolution: 2.2→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 36 50 3486
Biso mean--98.08 61.34 -
Num. residues----450
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1460SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1023HARMONIC5
X-RAY DIFFRACTIONt_it6672HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion473SEMIHARMONIC5
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_contact6912SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6672HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg11993HARMONIC2.20.8
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion15.24
LS refinement shellResolution: 2.2→2.31 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2649 134 4.49 %
Rwork0.2425 2852 -
all0.2435 2986 -
obs--99.97 %
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)
12.7353-1.1234-0.57424.65240.75172.5838-0.0432-0.02670.23340.02110.0197-0.0794-0.19550.06380.0235-0.020.0042-0.0898-0.1080.06670.0265-8.8619-16.1177104.5945
21.3753-0.01310.60512.8517-1.83194.07030.0880.0564-0.0308-0.1359-0.3117-0.31830.49030.34760.2237-0.11850.04560.0456-0.12990.0281-0.0007-14.2001-17.052189.6661
31.61350.1730.80561.8492-0.04272.2492-0.05370.4142-0.1007-0.4099-0.10070.03110.36610.28540.1544-0.08280.06930.0678-0.0390.018-0.1091-12.5604-8.498675.0084
42.9069-2.48020.15474.9506-2.5872.43150.04860.0368-0.13920.0519-0.1258-0.0101-0.05080.09870.07710.2040.0819-0.1148-0.19440.0354-0.08175.1608-1.9688115.8501
57.3911-2.3698-3.00353.59042.1677.10660.04840.13160.38610.04130.2921-0.025-0.3122-0.2657-0.3406-0.19160.0620.016-0.07370.1038-0.04427.45165.710685.2893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|43 - 89}A43 - 89
2X-RAY DIFFRACTION2{A|90 - 213}A90 - 213
3X-RAY DIFFRACTION3{A|214 - 354}A214 - 354
4X-RAY DIFFRACTION4{A|355 - 439}A355 - 439
5X-RAY DIFFRACTION5{A|440 - 507}A440 - 507

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