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- PDB-4mx9: CDPK1 from Neospora caninum in complex with inhibitor UW1294 -

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Basic information

Entry
Database: PDB / ID: 4mx9
TitleCDPK1 from Neospora caninum in complex with inhibitor UW1294
ComponentsCalmodulin-like domain protein kinase isoenzyme gamma, related
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-2E8 / Calmodulin-like domain protein kinase isoenzyme gamma, related
Similarity search - Component
Biological speciesNeospora caninum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsMerritt, E.A.
Citation
Journal: Plos One / Year: 2014
Title: Neospora caninum Calcium-Dependent Protein Kinase 1 Is an Effective Drug Target for Neosporosis Therapy.
Authors: Ojo, K.K. / Reid, M.C. / Kallur Siddaramaiah, L. / Muller, J. / Winzer, P. / Zhang, Z. / Keyloun, K.R. / Vidadala, R.S. / Merritt, E.A. / Hol, W.G. / Maly, D.J. / Fan, E. / Van Voorhis, W.C. / Hemphill, A.
#1: 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.
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Calmodulin-like domain protein kinase isoenzyme gamma, related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5002
Polymers55,0841
Non-polymers4171
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.380, 73.141, 66.270
Angle α, β, γ (deg.)90.000, 99.840, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as AU

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Components

#1: Protein Calmodulin-like domain protein kinase isoenzyme gamma, related


Mass: 55083.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neospora caninum (eukaryote) / Strain: Liverpool / Gene: CDPK1, NCLIV_011980, XP_003880764 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F0V9W9, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-2E8 / 3-(6-ethoxynaphthalen-2-yl)-1-[(1-methylpiperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 416.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM UW1294, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 ...Details: protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM UW1294, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 M BisTris pH 5.3, 5 mM DTT, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 3.1→65.3 Å / Num. obs: 7664 / % possible obs: 91.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.264 / Net I/σ(I): 4.5
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1 / Redundancy: 2.6 %

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
3.1-3.311.53714140492.6
8.77-65.39.192735190.7

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4M97

4m97


Resolution: 3.1→48.76 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.845 / WRfactor Rfree: 0.2885 / WRfactor Rwork: 0.2485 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7611 / SU B: 67.99 / SU ML: 0.541 / SU R Cruickshank DPI: 0.6214 / SU Rfree: 0.6739 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.674 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 336 4.7 %RANDOM
Rwork0.2491 ---
obs0.2502 7197 85.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 209.04 Å2 / Biso mean: 78.5996 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0 Å22.75 Å2
2--2.3 Å20 Å2
3----4.52 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 31 24 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193813
X-RAY DIFFRACTIONr_bond_other_d0.0020.023665
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9795145
X-RAY DIFFRACTIONr_angle_other_deg0.9343.0038464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61824.945182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4815725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.011521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
X-RAY DIFFRACTIONr_mcbond_it1.8932.721848
X-RAY DIFFRACTIONr_mcbond_other1.8932.721847
X-RAY DIFFRACTIONr_mcangle_it3.3714.0682310
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 9 -
Rwork0.398 418 -
all-427 -
obs--66.93 %
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)
10.27290.63050.01671.75780.42063.53080.0634-0.0878-0.0887-0.068-0.20240.1002-0.2851-0.10140.1390.4810.0521-0.03480.4475-0.00050.4864.1394-21.115-30.0476
21.19720.6884-0.79912.18310.15861.44190.1544-0.06390.09160.368-0.3121-0.14720.0242-0.10050.15780.552-0.0716-0.07930.5247-0.00340.38597.8133-14.5137-8.2019
31.0186-0.34810.99990.7725-0.48251.2788-0.2059-0.47090.4524-0.5053-0.367-0.47420.3875-0.72880.57291.2267-0.11110.31751.0996-0.0980.4651-10.3817-7.6483-29.7512
40.0443-0.1185-0.19040.65521.03321.69950.1473-0.0601-0.003-0.12260.2727-0.2497-0.28370.2177-0.41990.78180.1349-0.13330.81580.11180.3545-10.2116-11.144-53.7662
52.58340.0466-1.13782.1731.82642.07290.50560.09510.76060.6627-0.5670.47120.3114-0.5050.06141.0395-0.0145-0.18980.59-0.14910.6305-20.8527-7.8004-49.1858
65.64793.5788-4.21996.3091-1.08483.93680.3059-0.01550.46730.0618-0.02490.097-0.0329-0.1834-0.2810.5386-0.05250.05730.515-0.10340.4565-16.95862.7402-21.0757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 212
2X-RAY DIFFRACTION2A213 - 313
3X-RAY DIFFRACTION3A314 - 373
4X-RAY DIFFRACTION4A374 - 405
5X-RAY DIFFRACTION5A406 - 439
6X-RAY DIFFRACTION6A440 - 506

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