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- PDB-3i7c: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3i7c
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NA-PP2
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / protein kinase / calmodulin / EF hand / bumped kinase inhibitor / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane
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 ...: / 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-BK2 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors.
Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C. ...Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C.L. / Buckner, F.S. / Parsons, M. / Hol, W.G. / Merritt, E.A. / Van Voorhis, W.C.
#1: Journal: ACS Med Chem Lett / Year: 2010
Title: Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii.
Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)56,2952
Polymers55,9771
Non-polymers3171
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.139, 72.522, 67.116
Angle α, β, γ (deg.)90.00, 103.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 55977.227 Da / Num. of mol.: 1 / Fragment: residues 30-507
Source method: isolated from a genetically manipulated source
Details: residues 1-29 were replaced with a 3C cleavable His-tag and linker during cloning; tag was cleaved prior to crystallization
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TgCDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-BK2 / 1-tert-butyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine / 4-Amino-1-tert-butyl-3-(2-naphthyl)pyrazolo[3,4-d]pyrimidine


Mass: 317.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: 26% PEG 3350, 0.25 M ammonium citrate, 4 mM NA-PP2; directly frozen from mother liquor, pH 6.5, sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 30803 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.053 / Net I/σ(I): 9.2
Reflection shellResolution: 1.98→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.702 / Num. unique all: 2996 / Χ2: 1.088 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.95 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.39 Å
Translation2.5 Å39.39 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I79

3i79


Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 10.487 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1556 5.1 %RANDOM
Rwork0.193 ---
obs0.195 30780 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.37 Å2 / Biso mean: 26.071 Å2 / Biso min: 7.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.24 Å2
2---0.62 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 24 170 3906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223868
X-RAY DIFFRACTIONr_bond_other_d0.0010.022709
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.9775205
X-RAY DIFFRACTIONr_angle_other_deg0.7623.0016620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6595469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76424.839186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53715767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9231523
X-RAY DIFFRACTIONr_chiral_restr0.0560.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
X-RAY DIFFRACTIONr_mcbond_it1.38542311
X-RAY DIFFRACTIONr_mcbond_other0.3834948
X-RAY DIFFRACTIONr_mcangle_it2.33163741
X-RAY DIFFRACTIONr_scbond_it2.8561557
X-RAY DIFFRACTIONr_scangle_it4.492101459
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 118 -
Rwork0.255 2060 -
all-2178 -
obs--95.36 %
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)
12.295-1.64631.82344.9593-1.97984.3437-0.0865-0.10140.00540.33650.0005-0.2678-0.1220.12060.0860.08240.002-0.04110.1097-0.00950.132914.9113.27473.691
20.8368-0.2270.52421.2356-0.43072.2959-0.0008-0.02990.05690.0311-0.0283-0.06840.10460.0830.02910.07530.0054-0.00440.1165-0.00690.16168.48514.34259.092
31.6254-0.2188-0.14082.7760.48282.12040.04290.07040.0718-0.3051-0.0441-0.06070.00250.09780.00120.10540.0199-0.00880.130.00620.11025.47721.94441.085
40.67910.44141.52335.06356.05219.48330.02190.1394-0.19390.1856-0.0401-0.04770.44380.00410.01820.0852-0.03640.10680.1986-0.06180.300522.08722.53648.852
56.311-4.57577.36428.2666-7.062112.8717-0.3588-0.6129-0.18480.37970.7590.3511-0.8221-0.9157-0.40020.16630.13590.01230.14820.02540.063824.17632.1186.906
61.1772-1.46991.56711.9793-2.65986.42580.10470.1124-0.0291-0.0729-0.1649-0.03530.09490.44460.06020.10890.0251-0.07680.1211-0.01970.131431.85825.78481.877
75.6816-1.7858-1.05111.05230.9563.9919-0.0430.27870.20780.09150.04770.059-0.3040.0292-0.00470.08430.01380.00640.11780.00940.215330.19738.02653.113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 84
2X-RAY DIFFRACTION2A85 - 210
3X-RAY DIFFRACTION3A211 - 312
4X-RAY DIFFRACTION4A313 - 353
5X-RAY DIFFRACTION5A354 - 394
6X-RAY DIFFRACTION6A395 - 441
7X-RAY DIFFRACTION7A442 - 507

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