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

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Basic information

Entry
Database: PDB / ID: 3upx
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1300
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / calcium ion binding / ATP binding
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 / Phosphorylase Kinase; 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-B6A / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMerritt, E.A. / Larson, E.T.
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.M.J. / Buckner, F.S. / Parsons, M. / Hol, W.G.J. / 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.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G. ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G.J. / Buckner, F.S. / Napuli, A.J. / White, C.A. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)55,5612
Polymers55,2271
Non-polymers3341
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.290, 72.930, 66.920
Angle α, β, γ (deg.)90.000, 101.020, 90.000
Int Tables number4
Space group name H-MP1211

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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-B6A / [2-amino-1-(piperidin-4-ylmethyl)-1H-benzimidazol-6-yl](phenyl)methanone


Mass: 334.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1300, pH 7.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2011
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: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.271→39.743 Å / Num. all: 20869 / Num. obs: 20869 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rsym value: 0.089 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.27-2.394.10.6151.21235830030.61598.1
2.39-2.544.20.4041.91201428750.40498.2
2.54-2.714.20.3121.91113126690.31298.4
2.71-2.934.20.1734.41050225110.17398.6
2.93-3.214.20.1086.8977723460.10898.8
3.21-3.594.20.0817.6865620850.08199
3.59-4.154.10.0725.6778418760.07298.9
4.15-5.084.10.04314.6651815750.04399.1
5.08-7.184.10.04313.8507912350.04398.9
7.18-39.74340.04310.527646940.04398.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→36.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2777 / WRfactor Rwork: 0.2117 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8123 / SU B: 18.088 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3854 / SU Rfree: 0.2609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 1073 5.1 %RANDOM
Rwork0.2043 ---
obs0.2075 20868 98.58 %-
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: 119.8 Å2 / Biso mean: 52.067 Å2 / Biso min: 21.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å2-1.19 Å2
2---0.14 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.27→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 25 36 3581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023614
X-RAY DIFFRACTIONr_bond_other_d0.0010.022468
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9754870
X-RAY DIFFRACTIONr_angle_other_deg0.8163.0016003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.175445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47124.699166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52915668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1281520
X-RAY DIFFRACTIONr_chiral_restr0.0580.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 2.271→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 64 -
Rwork0.292 1398 -
all-1462 -
obs--97.47 %
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)
14.7642-1.33281.03365.0992-1.8794.1015-0.1123-0.06330.19040.37790.0266-0.1122-0.34160.07390.08570.2126-0.0326-0.0520.0506-0.04130.069419.8114.75540.271
21.9331-0.00240.28811.6368-0.95233.7805-0.0036-0.0141-0.0593-0.0379-0.0516-0.19710.03320.20840.05520.04730.0104-0.00180.0156-0.00570.128619.44913.02324.948
33.70420.3941-0.05282.6481-0.02482.1645-0.0530.3673-0.0245-0.3761-0.0394-0.11420.18360.1440.09250.07750.02960.01820.0903-0.00190.012417.58320.6548.408
40.2263-0.6669-2.68644.18410.855535.87970.06160.0653-0.0240.4897-0.1238-0.10620.1656-0.80840.06220.24870.0493-0.06490.20620.03680.18933.70233.49836.073
53.8796-1.2382-1.743710.01050.85382.05620.00680.2156-0.18370.3129-0.0175-0.16270.1968-0.15440.01070.54860.0342-0.17750.32810.00870.371836.9927.48353.377
69.7832-3.2385-2.96044.22582.68226.95920.10780.00980.48880.07880.1422-0.1354-0.41080.0655-0.25010.0479-0.0032-0.00450.02840.04760.124640.23136.53621.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 99
2X-RAY DIFFRACTION2A100 - 214
3X-RAY DIFFRACTION3A215 - 335
4X-RAY DIFFRACTION4A336 - 363
5X-RAY DIFFRACTION5A364 - 436
6X-RAY DIFFRACTION6A437 - 507

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