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- PDB-5jms: Crystal structure of TgCDPK1 bound to CGP060476 -

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Basic information

Entry
Database: PDB / ID: 5jms
TitleCrystal structure of TgCDPK1 bound to CGP060476
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-6LP / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 TgCDPK1bount to CGP060476
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 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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)60,0385
Polymers59,5331
Non-polymers5054
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.169, 72.750, 65.276
Angle α, β, γ (deg.)90.000, 98.620, 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 / Plasmid: pFBOH-MHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BJF5
#2: Chemical ChemComp-6LP / N~1~-(4-{2-[(3-chlorophenyl)amino]pyrimidin-4-yl}pyridin-2-yl)ethane-1,2-diamine


Mass: 340.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17ClN6
#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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
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: 2.3→50 Å / Num. obs: 19860 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 59.32 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Χ2: 1.648 / Net I/av σ(I): 38.577 / Net I/σ(I): 13.7 / Num. measured all: 101447
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.3450.631199.4
2.34-2.385.20.525199.5
2.38-2.435.10.444199
2.43-2.485.20.397199.9
2.48-2.535.10.352199.1
2.53-2.595.10.297199.6
2.59-2.665.10.251199.6
2.66-2.735.10.194199.4
2.73-2.815.10.171199.5
2.81-2.95.10.1421100
2.9-35.20.111199.8
3-3.125.10.092199.8
3.12-3.265.10.074199.8
3.26-3.445.10.06199.8
3.44-3.655.10.055199.8
3.65-3.935.10.053199.9
3.93-4.335.10.051199.9
4.33-4.955.10.041199.9
4.95-6.245.10.0371100
6.24-504.90.034198.6

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Processing

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

4ih8


Resolution: 2.3→48.28 Å / Cor.coef. Fo:Fc: 0.9276 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.369 / SU Rfree Blow DPI: 0.246
RfactorNum. reflection% reflectionSelection details
Rfree0.264 968 4.88 %RANDOM
Rwork0.2242 ---
obs0.2262 19850 99.57 %-
Displacement parametersBiso max: 175.12 Å2 / Biso mean: 74.11 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-7.5305 Å20 Å24.3983 Å2
2--5.9185 Å20 Å2
3----13.449 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.3→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 45 48 3466
Biso mean--102.53 58.76 -
Num. residues----447
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1468SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1019HARMONIC5
X-RAY DIFFRACTIONt_it6688HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
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_contact7017SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6688HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12026HARMONIC30.66
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion14.63
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2432 158 5.48 %
Rwork0.2267 2726 -
all0.2276 2884 -
obs--98.83 %
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)
12.7819-0.9756-0.39596.23020.27233.6023-0.0489-0.04560.17930.08760.0023-0.1353-0.16040.16410.0466-0.06590.0035-0.1027-0.09750.06740.0704-9.6385-15.6021104.7264
21.0762-0.14210.58292.8985-2.03434.01090.0933-0.0478-0.0584-0.1675-0.3397-0.37870.47710.39840.2463-0.13640.0520.0587-0.10860.02780.033-14.1896-17.425289.9285
31.2290.28251.04552.05910.20162.2822-0.0460.3694-0.0553-0.2362-0.0928-0.08470.32470.30990.1388-0.17270.07860.0747-0.07580.0267-0.0783-10.4701-7.080480.7436
41.4107-2.4055-1.69862.8836-1.0318-0.260.00760.0742-0.08360.0735-0.0667-0.03940.0592-0.03540.05910.12280.1336-0.147-0.1250.08420.04895.2876-4.8914114.2389
57.1694-2.1838-3.00543.66341.63876.8990.05230.08720.34440.10370.2654-0.0555-0.3214-0.189-0.3177-0.19320.0611-0.0137-0.05090.1056-0.03477.1995.372885.733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|44 - 90}A44 - 90
2X-RAY DIFFRACTION2{A|91 - 213}A91 - 213
3X-RAY DIFFRACTION3{A|214 - 376}A214 - 376
4X-RAY DIFFRACTION4{A|377 - 437}A377 - 437
5X-RAY DIFFRACTION5{A|438 - 507}A438 - 507

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