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- PDB-3t3v: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3t3v
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with Bumped Kinase Inhibitor, RM-1-87
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-BK4 / 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 25, 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)55,6223
Polymers55,2271
Non-polymers3952
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.973, 71.934, 66.621
Angle α, β, γ (deg.)90.000, 103.470, 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-BK4 / 3-(6-methoxynaphthalen-2-yl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine / RM-1-87


Mass: 333.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N5O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 39.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-87; 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 2, 2009
Diffraction measurementDetails: 1.00 degrees, 5.0 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: 0.076 / Number: 105552
ReflectionResolution: 2.04→50 Å / Num. obs: 28208 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 17.476
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.709 / Rsym value: 0.732 / % possible all: 99.9
Cell measurementReflection used: 105552

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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 3i79

3i79


Resolution: 2.04→39.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 10.677 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 1470 5.2 %RANDOM
Rwork0.1967 ---
obs0.199 28140 99.85 %-
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: 98.85 Å2 / Biso mean: 41.2153 Å2 / Biso min: 13.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.08 Å2
2---1.19 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.04→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 29 96 3757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223749
X-RAY DIFFRACTIONr_bond_other_d0.0030.022593
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.9715037
X-RAY DIFFRACTIONr_angle_other_deg1.0033.0016329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5935458
X-RAY DIFFRACTIONr_chiral_restr0.0570.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
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 (%)
2.04-2.0930.2971100.2771913202699.852
2.093-2.150.3011100.2611841195299.949
2.15-2.2120.2641100.24418071917100
2.212-2.280.278990.23717371836100
2.28-2.3550.293750.2211689176599.943
2.355-2.4370.286940.2151650174599.943
2.437-2.5290.233960.2091566166399.94
2.529-2.6310.255820.2281519160299.938
2.631-2.7480.268670.2341471154299.741
2.748-2.8810.285790.2111401148599.663
2.881-3.0360.199670.20113181385100
3.036-3.2190.231630.2051262132699.925
3.219-3.440.249620.2051164122899.837
3.44-3.7130.253620.1951081114499.913
3.713-4.0640.222530.1681001105599.905
4.064-4.5370.172620.14788694999.895
4.537-5.2270.218380.15480584999.293
5.227-6.3740.255450.18765570599.291
6.374-8.8970.179190.167527546100
8.897-39.1430.24130.15428630299.007
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)
12.6736-1.90881.54042.9401-1.44173.5941-0.1818-0.09620.15010.4008-0.0174-0.1341-0.52520.02670.19930.1992-0.0278-0.07420.0815-0.01160.06711.910616.094572.3454
20.8872-0.34650.17982.1402-0.52662.52390.0246-0.01890.01940.043-0.0962-0.20020.05150.14650.07160.0772-0.005-0.0140.1192-0.01020.13569.730613.587857.3748
31.7818-0.36420.07732.77620.38331.67680.08710.20760.0454-0.5088-0.1213-0.15940.01580.14190.03420.13330.03960.01810.12560.00430.05018.214720.85439.9187
40.2877-0.1159-1.37081.54134.32117.4041-0.06040.0493-0.02970.18440.1089-0.14380.1242-0.0256-0.04850.20680.0869-0.06880.10790.03360.173524.253333.715868.785
54.7885-3.1571-0.39537.46270.22644.9327-0.1160.0610.0253-0.14690.05810.0998-0.1345-0.07660.05790.21490.0562-0.11730.0552-0.01660.07129.337327.387986.3207
66.4729-1.8852-1.76552.01861.14664.49780.01710.01590.24690.16740.17380.0656-0.20710.0688-0.19090.05850.0065-0.00590.07750.03840.16130.634737.274353.5981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 95
2X-RAY DIFFRACTION2A96 - 214
3X-RAY DIFFRACTION3A215 - 334
4X-RAY DIFFRACTION4A335 - 364
5X-RAY DIFFRACTION5A365 - 435
6X-RAY DIFFRACTION6A436 - 507

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