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- PDB-5dvr: Crystal Structure of TgCDPK1 From Toxoplasma Gondii complexed wit... -

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Basic information

Entry
Database: PDB / ID: 5dvr
TitleCrystal Structure of TgCDPK1 From Toxoplasma Gondii complexed with GW780159X
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / CDPKs / Serine/Threonine Protein Kinase / Nucleotide-Binding / GW780159X
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-5G9 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / 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 GW780159X
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Osman, K.T.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: 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 / diffrn_radiation_wavelength / 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)59,8729
Polymers59,5331
Non-polymers3398
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.960, 72.456, 65.671
Angle α, β, γ (deg.)90.000, 98.220, 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: PET15_MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BJF5
#2: Chemical ChemComp-5G9 / 4-(3-chlorophenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine / GW780159X


Mass: 338.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11ClN4S
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 35.16 %
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: 2.4→72.46 Å / Num. obs: 17270 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.031 / Net I/σ(I): 17 / Num. measured all: 63430 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.493.40.7451.7573916730.7050.46192.4
8.98-72.4630.024438272740.9970.01776.7

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KU2

3ku2


Resolution: 2.4→31.644 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.58 / Stereochemistry target values: ML
Details: This structure model was refined and adjusted using 3KU2, a structure model of the same protein complexed with ANP, as a template. It contains disjoint segments around residues 358, 377 and ...Details: This structure model was refined and adjusted using 3KU2, a structure model of the same protein complexed with ANP, as a template. It contains disjoint segments around residues 358, 377 and 405, and the main chain torsion angles are remarkably poor in these residues. There are also other gaps in the protein chain and poorly resolved loops which are easy to misinterpret. Whoever analyzes the structure needs to consider the risk of out-of-register errors under these circumstances, and is recommended to refer to the electron density map for model credibility.
RfactorNum. reflection% reflection
Rfree0.299 850 4.93 %
Rwork0.2303 16400 -
obs0.2338 17250 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.25 Å2 / Biso mean: 65.1642 Å2 / Biso min: 33.78 Å2
Refinement stepCycle: final / Resolution: 2.4→31.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 30 3 2806
Biso mean--64.23 48.01 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092857
X-RAY DIFFRACTIONf_angle_d1.143886
X-RAY DIFFRACTIONf_chiral_restr0.042452
X-RAY DIFFRACTIONf_plane_restr0.005528
X-RAY DIFFRACTIONf_dihedral_angle_d13.088964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.550.3861310.29672628275995
2.55-2.74680.3391500.292327152865100
2.7468-3.0230.32851380.265427942932100
3.023-3.460.30951350.245327752910100
3.46-4.35740.27031700.21172735290599
4.3574-31.6470.29451260.21162753287997

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