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- PDB-3n51: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3n51
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor RM-1-95
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / bumped kinase inhibitor / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / 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-BK3 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
Citation
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.
#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
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_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_ref_seq_dif.details / _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-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7404
Polymers55,2271
Non-polymers5133
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.523, 72.754, 66.024
Angle α, β, γ (deg.)90.000, 98.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 55226.914 Da / Num. of mol.: 1 / Fragment: TgCDPK1, 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: AAG53993, CDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-BK3 / 3-(naphthalen-1-ylmethyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 372.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N6
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), pH 6.5, VAPOR ...Details: 24% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26020 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 3.8 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.002 / Net I/σ(I): 6.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2590 / Χ2: 0.989 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3i7b

3i7b


Resolution: 2.1→39.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.388 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1325 5.1 %RANDOM
Rwork0.193 ---
obs0.196 26002 99.88 %-
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: 116.81 Å2 / Biso mean: 50.291 Å2 / Biso min: 21.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.87 Å2
2--0.41 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 36 93 3742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223767
X-RAY DIFFRACTIONr_bond_other_d0.0010.022638
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.985072
X-RAY DIFFRACTIONr_angle_other_deg0.8013.0026420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1825462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6724.835182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3771522
X-RAY DIFFRACTIONr_chiral_restr0.0620.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_mcbond_it1.75442246
X-RAY DIFFRACTIONr_mcbond_other0.5444922
X-RAY DIFFRACTIONr_mcangle_it2.74763634
X-RAY DIFFRACTIONr_scbond_it3.50961521
X-RAY DIFFRACTIONr_scangle_it5.099101430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1550.3391070.2621785191199.006
2.155-2.2140.285890.2241770186099.946
2.214-2.2780.292760.221763184299.837
2.278-2.3480.258780.19116731751100
2.348-2.4240.242830.20616131696100
2.424-2.5090.261750.21315781653100
2.509-2.6030.274750.2021496157299.936
2.603-2.7090.284730.19714571530100
2.709-2.8290.228800.1841411149299.933
2.829-2.9660.214660.1711330139799.928
2.966-3.1260.263640.19612831347100
3.126-3.3140.258580.1971209126899.921
3.314-3.5410.249770.19711161193100
3.541-3.8220.246560.18410721128100
3.822-4.1830.231680.1719611029100
4.183-4.670.184600.16287994099.894
4.67-5.380.267510.19277883199.759
5.38-6.5590.221380.21567071099.718
6.559-9.150.212290.189522551100
9.15-39.4510.194220.189311333100
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)
13.2186-1.22641.51012.5579-2.54735.9967-0.1762-0.16280.34260.41860.0313-0.1502-0.66290.06480.14480.16150.0008-0.03540.0194-0.00180.085817.522916.335273.2996
20.372-0.5029-0.44722.5074-1.1263.2272-0.0923-0.1102-0.10770.23080.06760.1989-0.0951-0.20920.02470.08280.05940.00650.20260.03610.077310.202212.078668.2295
31.8289-0.13040.09291.7941-0.96521.91410.1093-0.0111-0.0273-0.0833-0.184-0.08410.14030.27530.07480.12630.0383-0.00420.10520.01440.117217.204515.383152.6989
42.0004-0.58080.10532.0994-0.09681.91150.09840.2397-0.0227-0.3977-0.12070.04770.17050.19220.02240.10090.0434-0.02560.0956-0.00390.04311.685621.881540.8204
51.1564-0.0220.63165.98013.815.52120.01870.2523-0.14910.1437-0.10490.16010.35350.160.08620.03760.04920.03330.22790.02580.144728.333922.492148.6979
67.8035-4.2935-1.24879.41511.28384.69540.30260.4291-0.49890.2772-0.340.33550.0352-0.53420.03750.1734-0.020.00170.0859-0.03890.051537.30730.704286.9523
78.5522-5.9557-0.02054.6317-1.66275.92261.13631.03010.1546-0.9087-0.8369-0.0460.45280.4937-0.29940.35460.1821-0.02840.2161-0.04630.081343.49130.920183.8672
83.3288-0.9421-0.90483.61650.6453.2787-0.0215-0.04380.1610.17230.24740.0671-0.1738-0.0899-0.22590.04390.0247-0.02030.08790.04010.105535.883537.919854.4131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 93
2X-RAY DIFFRACTION2A94 - 134
3X-RAY DIFFRACTION3A135 - 213
4X-RAY DIFFRACTION4A214 - 313
5X-RAY DIFFRACTION5A314 - 353
6X-RAY DIFFRACTION6A354 - 416
7X-RAY DIFFRACTION7A417 - 435
8X-RAY DIFFRACTION8A436 - 507

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