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- PDB-3khe: Crystal structure of the calcium-loaded calmodulin-like domain of... -

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Basic information

Entry
Database: PDB / ID: 3khe
TitleCrystal structure of the calcium-loaded calmodulin-like domain of the CDPK, 541.m00134 from toxoplasma gondii
ComponentsCalmodulin-like domain protein kinase isoform 3
KeywordsMETAL BINDING PROTEIN / calcium dependent kinase / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
EF-hand / Recoverin; 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 / Serine/threonine-protein kinase, active site ...EF-hand / Recoverin; 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-dependent protein kinase CDPK3
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Artz, J.D. / Mackenzie, F. / Cossar, D. / Kozieradzki, I. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Wernimont, A.K. / Hutchinson, A. / Artz, J.D. / Mackenzie, F. / Cossar, D. / Kozieradzki, I. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Qiu, W. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2011
Title: Structures of parasitic CDPK domains point to a common mechanism of activation.
Authors: Wernimont, A.K. / Amani, M. / Qiu, W. / Pizarro, J.C. / Artz, J.D. / Lin, Y.H. / Lew, J. / Hutchinson, A. / Hui, R.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Calmodulin-like domain protein kinase isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,35516
Polymers43,6852
Non-polymers67014
Water6,557364
1
A: Calmodulin-like domain protein kinase isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0276
Polymers21,8421
Non-polymers1855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calmodulin-like domain protein kinase isoform 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,32810
Polymers21,8421
Non-polymers4859
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.838, 101.015, 107.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21842.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGME49_105860 / Plasmid: pet15mlh / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3HNM6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24 % PEG3350, 0.1 M NH4SO4, 0.1 M BisTris 6.5, 2 mM CaCl2, 4 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 37365 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.156 / Χ2: 1.161 / Net I/σ(I): 3.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 2.58 / Num. unique all: 2468 / Rsym value: 0.64 / Χ2: 0.955 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
JBluIce-EPICSdata collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.732 / SU B: 8.879 / SU ML: 0.115 / SU R Cruickshank DPI: 0.399 / SU Rfree: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1864 5 %RANDOM
Rwork0.201 ---
all0.204 37348 --
obs0.204 37266 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 111.25 Å2 / Biso mean: 21.546 Å2 / Biso min: 3.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--1.82 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 29 364 3380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0213222
X-RAY DIFFRACTIONr_bond_other_d0.0010.022165
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9594356
X-RAY DIFFRACTIONr_angle_other_deg1.07235325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3745416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99126.18178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05815615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8991516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023716
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02625
X-RAY DIFFRACTIONr_mcbond_it1.5961.51962
X-RAY DIFFRACTIONr_mcbond_other0.5131.5812
X-RAY DIFFRACTIONr_mcangle_it2.4823168
X-RAY DIFFRACTIONr_scbond_it4.50331260
X-RAY DIFFRACTIONr_scangle_it6.6274.51180
X-RAY DIFFRACTIONr_rigid_bond_restr1.99435387
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 151 -
Rwork0.221 2529 -
all-2680 -
obs-3683 98.46 %
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)
12.1785-1.0021-4.40146.77926.489912.05990.483-0.23260.1659-0.3638-0.0519-0.1902-1.06130.3798-0.4310.1535-0.04360.00980.1224-0.00880.054111.184316.44815.7064
20.5165-0.459-0.54310.980.65290.6622-0.0255-0.05560.0022-0.0243-0.03220.01210.02670.0110.05770.0686-0.003-0.00030.11080.00870.090110.91250.50828.8054
31.1857-0.4527-0.58620.79020.34061.44440.0667-0.06740.0801-0.0230.0144-0.0008-0.1978-0.0726-0.08110.10150.00430.00620.06560.00990.0780.664314.590313.8472
41.1162-4.8487-2.375928.13260.415219.0550.09580.14160.04510.8576-0.6763-0.5625-1.4377-0.01470.58060.33780.08540.02950.16550.13880.13191.28428.55453.1697
50.5895-0.2783-0.19850.28150.21360.16770.04610.07270.0657-0.0312-0.0439-0.0329-0.0213-0.0318-0.00220.0771-0.00110.00110.09790.01170.09559.45426.15596.262
60.4941-0.0506-0.28270.22710.26931.27840.00810.0533-0.0112-0.02060.0151-0.0145-0.0008-0.0855-0.02330.0729-0.0009-0.00010.09720.01280.078318.0283-5.7526-2.7033
72.05972.06793.33066.17736.933110.66570.31060.0778-0.2150.3517-0.0388-0.26040.63180.1783-0.27170.11180.0365-0.02220.04390.01990.0902-12.0657-17.599222.345
80.61690.43310.42410.90060.04920.45050.0173-0.0118-0.00490.00680.01130.00760.07240.0059-0.02860.0809-0.00170.00150.08320.00420.0784-18.1223-8.580617.4871
94.286412.93541.774142.165310.21238.3145-0.14810.0075-0.4814-0.76290.1372-1.291-0.64740.27660.01090.1254-0.07590.0220.1399-0.04010.0916-22.0274-30.301919.6836
100.12620.89020.110613.2133-1.59431.0030.095-0.04870.01280.3355-0.2061-0.01320.09380.02360.11110.1153-0.0701-0.01530.17820.06780.0797-20.2774-17.707530.4472
110.52480.54220.08140.73270.25310.35520.00490.0307-0.00750.01680.0069-0.0121-0.00740.0212-0.01180.07870.0122-0.00390.08980.00380.0854-9.6561-0.101320.3031
120.40890.08720.08050.25650.05520.9224-0.0018-0.0854-0.01970.00780.02230.0125-0.0018-0.0071-0.02040.07530.0009-0.00270.08980.00780.0829-4.57564.593932.5533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 18
2X-RAY DIFFRACTION2A19 - 37
3X-RAY DIFFRACTION3A38 - 63
4X-RAY DIFFRACTION4A64 - 88
5X-RAY DIFFRACTION5A89 - 130
6X-RAY DIFFRACTION6A131 - 191
7X-RAY DIFFRACTION7B1 - 18
8X-RAY DIFFRACTION8B19 - 63
9X-RAY DIFFRACTION9B64 - 77
10X-RAY DIFFRACTION10B78 - 100
11X-RAY DIFFRACTION11B101 - 139
12X-RAY DIFFRACTION12B140 - 191

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