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

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Basic information

Entry
Database: PDB / ID: 3sxf
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with Bumped Kinase Inhibitor, RM-1-89
ComponentsCalmodulin-domain protein kinase 1
Keywordstransferase/transferase inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / EF hand / bumped kinase inhibitor / 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-BK5 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 Å
AuthorsLarson, E.T. / Merritt, E.A.
Citation
Journal: J.Med.Chem. / Year: 2012
Title: Multiple determinants for selective inhibition of apicomplexan calcium-dependent protein kinase CDPK1.
Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / ...Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / Verlinde, C.L. / Fan, E. / Van Voorhis, W.C. / Maly, D.J. / Merritt, E.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.
#2: 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 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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

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Assembly

Deposited unit
A: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7154
Polymers55,2271
Non-polymers4883
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.446, 72.238, 65.815
Angle α, β, γ (deg.)90.000, 99.180, 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-domain protein kinase 1 / Calmodulin-domain protein kinase / putative


Mass: 55226.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-29 were replaced with a cleavable His-tag plus linker during cloning; tag was cleaved prior to crystallization
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: AAG53993, CDPK1, TGGT1_059880, TGVEG_042030 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-BK5 / 3-(6-ethoxynaphthalen-2-yl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine / RM-1-89


Mass: 347.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N5O
#3: Chemical ChemComp-DMS / 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


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 26% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-89; mother liquor supplemented with 10% ethylene glycol prior to freezing in LN2, pH 7.0, 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: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
Diffraction measurementDetails: 1.00 degrees, 4.0 sec, detector distance 300.00 mm
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.965 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionAv R equivalents: 0.064 / Number: 105862
ReflectionResolution: 2.04→50 Å / Num. obs: 28166 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 21.496
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.695 / % possible all: 99.2
Cell measurementReflection used: 105862

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.6.0095refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3I7B

3i7b


Resolution: 2.04→39.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 11.032 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1432 5.1 %RANDOM
Rwork0.2008 ---
obs0.2026 28099 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 124.63 Å2 / Biso mean: 50.8917 Å2 / Biso min: 23.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.38 Å2
2--2.44 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.04→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 34 76 3724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223772
X-RAY DIFFRACTIONr_bond_other_d0.0010.022596
X-RAY DIFFRACTIONr_angle_refined_deg0.851.9685075
X-RAY DIFFRACTIONr_angle_other_deg0.7353.0016327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5595463
X-RAY DIFFRACTIONr_chiral_restr0.0490.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
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 (%)
2.038-2.0910.311970.2921883200298.901
2.091-2.1480.2951130.26918461959100
2.148-2.210.273960.24118161912100
2.21-2.2780.254730.23717761849100
2.278-2.3520.291900.21516861776100
2.352-2.4340.221750.211636171299.942
2.434-2.5260.299800.22615971677100
2.526-2.6290.252740.22415371611100
2.629-2.7450.242770.2121451152999.935
2.745-2.8780.213660.21914131479100
2.878-3.0330.255790.20512861365100
3.033-3.2160.251560.2031269132799.849
3.216-3.4360.241730.2061168124299.919
3.436-3.7090.236570.1971083114199.912
3.709-4.060.239700.189831053100
4.06-4.5330.202590.16689795899.791
4.533-5.2220.247490.182791840100
5.222-6.3680.228400.20466070299.715
6.368-8.890.164320.1851354699.817
8.89-39.30.182190.1627330197.01
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)
11.8594-0.84041.14222.948-1.81116.5953-0.1202-0.15480.16620.2653-0.0863-0.107-0.26580.13170.20650.08660.0039-0.0120.03370.00620.130912.971314.134670.7336
21.0569-0.09620.44081.7477-1.6164.13480.0950.0854-0.0389-0.1298-0.323-0.18420.32210.47460.2280.12450.06820.00960.11030.03280.164616.481515.271755.4585
31.47750.06850.91951.63780.00912.18410.05340.3352-0.0511-0.2744-0.0751-0.03650.28760.33440.02170.13070.08610.01640.14870.0110.09416.14822.095343.5436
48.0548-6.6929-2.02548.27881.721912.02530.27970.6104-0.34360.2049-0.41010.4939-0.0759-0.30250.13040.2934-0.00570.00020.0605-0.01690.039238.826530.111186.3275
54.6977-0.6944-1.78182.98110.32983.47490.0408-0.00590.36120.21710.28840.1478-0.1809-0.0415-0.32920.05460.0395-0.02180.11860.05630.205435.508537.520254.6299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 119
2X-RAY DIFFRACTION2A120 - 213
3X-RAY DIFFRACTION3A214 - 356
4X-RAY DIFFRACTION4A357 - 434
5X-RAY DIFFRACTION5A435 - 507

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