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- PDB-9mi4: Crystal structure of calcium-dependent protein kinase 1 (CDPK1) f... -

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Basic information

Entry
Database: PDB / ID: 9mi4
TitleCrystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-3-115
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Cryptosporidium parvum / CDPK1
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...: / 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 / 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
Similarity search - Domain/homology
: / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor WIN-3-115.
Authors: Liu, L. / Cooper, A. / Lovell, S. / Battaile, K.P.
History
DepositionDec 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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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)57,3967
Polymers56,7101
Non-polymers6856
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.855, 56.641, 80.397
Angle α, β, γ (deg.)90.00, 103.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 56710.387 Da / Num. of mol.: 1 / Fragment: G70-E538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd3_920 / Plasmid: CrpaA.01010.b.GT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A3FQ16
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1BLB / (6M)-6-(2,4-dichlorophenyl)-8-(2-hydroxyethyl)-2-[3-(methanesulfonyl)anilino]pyrido[2,3-d]pyrimidin-7(8H)-one


Mass: 505.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18Cl2N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 27% (w/v) PEG 3350, 0.2M Ammonium Tartrate, 0.1M MES pH 6.0. . CrpaA.01010.b.GT4.PW39259 at 16.8 mg/mL. 2 mM inhibitor added prior to crystallization. plate 14388 well C3 drop 2, Puck: ...Details: 27% (w/v) PEG 3350, 0.2M Ammonium Tartrate, 0.1M MES pH 6.0. . CrpaA.01010.b.GT4.PW39259 at 16.8 mg/mL. 2 mM inhibitor added prior to crystallization. plate 14388 well C3 drop 2, Puck: PSL0107, Cryo: 30% (w/v) PEG 3350, 0.2M Ammonium Tartrate, 0.1M MES pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.94→78.03 Å / Num. obs: 11324 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.08 / Rrim(I) all: 0.185 / Χ2: 1.06 / Net I/σ(I): 7.9 / Num. measured all: 57882
Reflection shellResolution: 2.94→3.02 Å / % possible obs: 100 % / Redundancy: 5.4 % / Rmerge(I) obs: 1.043 / Num. measured all: 4463 / Num. unique obs: 827 / CC1/2: 0.724 / Rpim(I) all: 0.483 / Rrim(I) all: 1.153 / Χ2: 0.88 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→78.03 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 534 4.72 %
Rwork0.199 --
obs0.2016 11304 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→78.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 38 0 3621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033686
X-RAY DIFFRACTIONf_angle_d0.5154976
X-RAY DIFFRACTIONf_dihedral_angle_d11.9131365
X-RAY DIFFRACTIONf_chiral_restr0.038558
X-RAY DIFFRACTIONf_plane_restr0.003637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.240.34291100.26752679X-RAY DIFFRACTION100
3.24-3.70.30471250.23932688X-RAY DIFFRACTION100
3.71-4.670.22131480.17012674X-RAY DIFFRACTION100
4.67-78.030.22741510.18312729X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.1512 Å / Origin y: 7.4389 Å / Origin z: 17.6168 Å
111213212223313233
T0.4338 Å2-0.0086 Å20.0324 Å2-0.2963 Å2-0.0184 Å2--0.3877 Å2
L2.352 °20.4409 °2-0.0479 °2-1.1164 °2-0.0938 °2--1.3255 °2
S-0.0493 Å °0.017 Å °-0.0276 Å °0.0742 Å °0.0076 Å °-0.0524 Å °0.0068 Å °0.1509 Å °0.0493 Å °
Refinement TLS groupSelection details: all

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