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- PDB-3dxn: Crystal structure of the calcium-dependent kinase from toxoplasma... -

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Basic information

Entry
Database: PDB / ID: 3dxn
TitleCrystal structure of the calcium-dependent kinase from toxoplasma gondii, 541.m00134, kinase domain.
ComponentsCalmodulin-like domain protein kinase isoform 3
KeywordsTRANSFERASE / cdpk / calcium dependent kinase / calmodulin / parasite / ATP-binding / Kinase / Nucleotide-binding / Structural Genomics / 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
Calcium-dependent protein kinase CDPK3
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsWernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Wasney, G. / Lin, Y.H. / Hassani, A. / Ali, A. / Schapira, M. / Bochkarev, A. ...Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Wasney, G. / Lin, Y.H. / Hassani, A. / Ali, A. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wikstrom, M. / Edwards, A.M. / Hui, R. / Artz, J.D. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the calcium-dependent kinase from toxoplasma gondii, 541.m00134, kinase domain.
Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Wasney, G. / Lin, Y.H. / Hassani, A. / Ali, A. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wikstrom, M. / ...Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Wasney, G. / Lin, Y.H. / Hassani, A. / Ali, A. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wikstrom, M. / Edwards, A.M. / Hui, R. / Amani, M.
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-like domain protein kinase isoform 3


Theoretical massNumber of molelcules
Total (without water)33,0251
Polymers33,0251
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.345, 121.345, 45.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Calmodulin-like domain protein kinase isoform 3


Mass: 33025.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: 541.m00134 / Plasmid: p15mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q3HNM6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2 M NaCl, 0.1 M Hepes, 5 % ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→85.75 Å / Num. all: 17797 / Num. obs: 17780 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.097 / Χ2: 1.074 / Net I/σ(I): 10.7
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.72 / Num. unique all: 1726 / Rsym value: 0.62 / Χ2: 0.774 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.34 Å
Translation2.5 Å30.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.81 / SU B: 14.633 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.255 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 904 5.1 %RANDOM
Rwork0.23 ---
all0.232 17784 --
obs0.232 17770 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.44 Å2 / Biso mean: 44.574 Å2 / Biso min: 29.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 66 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222091
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.9722833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3715263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34723.91392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49415364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6011512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021560
X-RAY DIFFRACTIONr_nbd_refined0.1570.2906
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0220.22
X-RAY DIFFRACTIONr_mcbond_it0.1521.51339
X-RAY DIFFRACTIONr_mcangle_it0.26722075
X-RAY DIFFRACTIONr_scbond_it0.3043867
X-RAY DIFFRACTIONr_scangle_it0.4324.5753
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 68 -
Rwork0.283 1207 -
all-1275 -
obs-1726 99.61 %
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)
116.1973-8.6425.236424.5136-1.48978.84450.1859-0.5671.45510.99860.4908-0.116-0.4402-0.2482-0.67670.130.09580.16170.0408-0.17180.334835.66139.201-21.391
213.1154-3.29792.279512.5443-7.481810.5188-0.2027-1.1318-0.00451.0040.28720.0341-0.6970.2654-0.08450.09730.16590.09840.1013-0.12760.094539.83934.385-17.153
34.48410.3075-0.62686.3811.81553.4865-0.1351-0.83870.4743-0.14720.2080.2136-0.4057-0.02-0.0729-0.08320.1270.04-0.04210.0604-0.069943.78127.978-26.25
49.7127-1.3632-1.22447.60161.58033.9157-0.1606-0.54240.3117-0.44070.20460.0045-0.21080.0226-0.044-0.14530.08580.033-0.16580.0135-0.208847.05622.358-29.038
56.78246.17162.08926.64970.27443.20290.014-1.8419-0.40890.8155-0.25510.52280.1827-0.48550.24110.03890.19050.13460.42490.16930.036242.9612.668-18.679
66.55172.02032.31254.24822.30157.5899-0.505-0.4432-0.4642-0.43750.08280.28250.1253-0.44820.4223-0.07560.06860.094-0.19880.0981-0.117339.6119.606-31.93
76.84881.093-6.44418.08051.501818.6104-0.4216-0.6809-0.73380.1254-0.17330.51370.3523-0.8860.59490.03870.02050.1126-0.05740.05010.249134.3152.665-30.915
88.67431.8877-2.0956.8927-0.51855.7453-0.87220.1621-1.2544-1.10160.6794-0.86540.36270.35840.19280.05690.02060.3049-0.2450.00720.117550.7397.884-36.756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 3420 - 34
2X-RAY DIFFRACTION2AA35 - 6635 - 66
3X-RAY DIFFRACTION3AA67 - 12567 - 125
4X-RAY DIFFRACTION4AA126 - 167126 - 167
5X-RAY DIFFRACTION5AA168 - 202168 - 202
6X-RAY DIFFRACTION6AA203 - 224203 - 224
7X-RAY DIFFRACTION7AA225 - 248225 - 248
8X-RAY DIFFRACTION8AA249 - 287249 - 287

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