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- PDB-4mxa: CDPK1 from Neospora caninum in complex with inhibitor RM-1-132 -

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Basic information

Entry
Database: PDB / ID: 4mxa
TitleCDPK1 from Neospora caninum in complex with inhibitor RM-1-132
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


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-BK7 / Calmodulin-like domain protein kinase isoenzyme gamma, related
Similarity search - Component
Biological speciesNeospora caninum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 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)55,4862
Polymers55,0841
Non-polymers4021
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.220, 72.530, 65.650
Angle α, β, γ (deg.)90.000, 99.280, 90.000
Int Tables number4
Space group name H-MP1211

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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-BK7 / 3-(6-ethoxynaphthalen-2-yl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine / RM-1-132


Mass: 402.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
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 RM-1-132, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0. ...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 RM-1-132, 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→47.59 Å / Num. obs: 8027 / % possible obs: 89.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.376 / Net I/σ(I): 3.6
Reflection shell

Rmerge(I) obs: 0.018 / Diffraction-ID: 1 / Redundancy: 2.7 %

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
3-3.2113820143289.7
8.49-47.5917.8105939593.1

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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→47.63 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.807 / WRfactor Rfree: 0.2815 / WRfactor Rwork: 0.2577 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7868 / SU B: 60.368 / SU ML: 0.555 / SU R Cruickshank DPI: 0.726 / SU Rfree: 0.6883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.688 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 328 4.6 %RANDOM
Rwork0.2526 ---
obs0.2538 7097 78.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.59 Å2 / Biso mean: 73.6112 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-0 Å20.4 Å2
2--0.97 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 3→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 30 25 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193812
X-RAY DIFFRACTIONr_bond_other_d0.0010.023663
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9785143
X-RAY DIFFRACTIONr_angle_other_deg0.8013.0018430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5335471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38924.945182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41215725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2911521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
X-RAY DIFFRACTIONr_mcbond_it1.5092.8611848
X-RAY DIFFRACTIONr_mcbond_other1.5072.8611847
X-RAY DIFFRACTIONr_mcangle_it2.6024.2892310
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 16 -
Rwork0.252 340 -
all-356 -
obs--56.51 %
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)
11.70030.02690.77073.14632.24794.8825-0.10550.14370.1364-0.3188-0.12970.2103-0.2547-0.34670.23520.20180.0405-0.06780.23320.06530.4593.6221-20.9994-29.5798
24.01011.1948-0.81177.2242-0.60893.83580.1084-0.51420.22820.6802-0.0505-0.22520.3695-0.27-0.05790.2173-0.0697-0.07440.2339-0.03870.20147.4516-14.2862-7.8703
31.253-0.55632.02612.0423-4.396212.1910.026-0.0558-0.2814-0.91550.06640.06361.7882-0.3787-0.09240.4861-0.12180.04510.3464-0.12170.6242-10.6819-7.5819-29.3315
419.52794.23211.49355.85545.52138.6322-1.2991-1.8817-1.0966-0.90971.7706-0.306-1.18930.1434-0.47141.2593-0.0088-0.09481.02930.05540.9213-10.7084-11.1201-53.483
55.4918-1.62590.378110.12583.83051.63760.05141.24271.70750.4967-0.81080.96090.2015-0.11150.75941.0412-0.3196-0.23440.51060.19741.2149-21.1922-7.7503-48.8579
613.20622.2883-3.46586.1426-0.2297.94250.33660.1980.9615-0.0117-0.04350.5479-0.44170.0893-0.29310.1659-0.0039-0.07250.0985-0.12130.4426-17.252.7479-20.7252
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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