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- PDB-3i7b: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -

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Basic information

Entry
Database: PDB / ID: 3i7b
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NM-PP1
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / protein kinase / calmodulin / EF hand / bumped kinase inhibitor / ATP-binding / kinase / nucleotide-binding / serine/threonine-protein kinase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
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-BK1 / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.988 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
Citation
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.
#1: Journal: ACS Med.chem.lett. / Year: 2010
Title: Discovery of Potent and Selective Inhibitors of 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.R. / Verlinde, C.L.M.J. / White Jr, A.C. / ...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.R. / Verlinde, C.L.M.J. / White Jr, A.C. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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)55,8096
Polymers55,2271
Non-polymers5825
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.243, 72.851, 65.713
Angle α, β, γ (deg.)90.00, 98.78, 90.00
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: 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: CDPK1, TgCDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-BK1 / 1-(1-methylethyl)-3-(naphthalen-1-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine / 4-Amino-1-iso-propyl-3-(1-naphthylmethyl)pyrazolo[3,4-d]pyrimidine


Mass: 317.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 39.22 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: 26% PEG 3350, 0.18 M ammonium citrate, 4 mM NM-PP1; cryoprotected with 10% ethylene glycol, pH 6.5, sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.988→50 Å / Num. obs: 30350 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 4.2 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.039 / Net I/σ(I): 8.3
Reflection shellResolution: 1.988→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2975 / Χ2: 1.07 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.21 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.72 Å
Translation2.5 Å35.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I79

3i79


Resolution: 1.988→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.825 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1536 5.1 %RANDOM
Rwork0.192 ---
obs0.194 30333 99.77 %-
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: 62.84 Å2 / Biso mean: 19.845 Å2 / Biso min: 3.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.78 Å2
2--0.67 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.988→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 40 127 3861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223850
X-RAY DIFFRACTIONr_bond_other_d0.0010.022699
X-RAY DIFFRACTIONr_angle_refined_deg0.8781.985177
X-RAY DIFFRACTIONr_angle_other_deg0.7493.0016581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5575472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8424.754183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53415753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4451523
X-RAY DIFFRACTIONr_chiral_restr0.050.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_mcbond_it0.98542301
X-RAY DIFFRACTIONr_mcbond_other0.2454945
X-RAY DIFFRACTIONr_mcangle_it1.72463723
X-RAY DIFFRACTIONr_scbond_it2.05461549
X-RAY DIFFRACTIONr_scangle_it3.245101446
LS refinement shellResolution: 1.988→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 105 -
Rwork0.251 2063 -
all-2168 -
obs--97.18 %
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)
12.4326-0.89651.01092.0606-1.6995.9522-0.0688-0.03960.1230.2363-0.0823-0.071-0.3340.17610.15110.2829-0.0106-0.02170.2750.01880.290119.20215.47773.654
21.002-0.0582-0.14451.0693-0.80963.43970.0197-0.0967-0.07390.0661-0.02130.0325-0.0119-0.05580.00160.24930.0357-0.00490.2263-0.00480.280614.80613.07860.359
32.7406-0.69980.42922.4496-0.84212.40990.0297-0.08530.08870.1426-0.0407-0.1023-0.06610.07560.0110.268-0.0019-0.00470.25550.0130.274613.72416.5855.635
41.6611-0.32440.04471.7110.1031.72940.02160.1664-0.0433-0.2757-0.03560.02930.14150.18180.0140.27060.0255-0.02240.3013-0.00470.267512.80320.44540.044
51.9386-0.04211.14184.08563.98889.2916-0.1423-0.0057-0.03940.2921-0.08940.12050.1244-0.02440.23170.21490.0130.01430.38250.02560.324429.59629.21354.704
68.5931-3.58650.46227.36210.21145.68570.15680.02560.07170.3938-0.37420.0359-0.1667-0.67230.21740.3086-0.01580.03460.2318-0.05570.125936.35634.13589.917
723.480224.636119.096529.539212.33763.9021-0.43570.7106-0.0473-2.08730.58171.7768-0.74060.636-0.1460.2676-0.0295-0.10560.8174-0.39870.85726.43527.86781.979
86.7771-4.5859-4.0894.12222.05975.83580.41250.9932-0.4917-0.362-0.78960.2539-0.0729-0.26730.37710.26380.0584-0.04540.3804-0.10350.19242.89527.52282.908
94.6303-2.0727-1.59654.47221.26332.7877-0.2108-0.1022-0.17880.29820.18950.10010.1826-0.03490.02130.18340.0186-0.04780.30550.01070.266334.85132.55853.203
102.88890.69720.84952.7076-1.21124.1213-0.0488-0.02750.2894-0.02070.0781-0.0318-0.39230.0064-0.02930.22610.0292-0.03290.2429-0.00250.319836.80744.10855.091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 88
2X-RAY DIFFRACTION2A89 - 155
3X-RAY DIFFRACTION3A156 - 213
4X-RAY DIFFRACTION4A214 - 323
5X-RAY DIFFRACTION5A324 - 355
6X-RAY DIFFRACTION6A356 - 382
7X-RAY DIFFRACTION7A383 - 397
8X-RAY DIFFRACTION8A401 - 435
9X-RAY DIFFRACTION9A436 - 474
10X-RAY DIFFRACTION10A475 - 507

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