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- PDB-9mi5: Crystal structure of calcium-dependent protein kinase 1 (CDPK1) f... -

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Basic information

Entry
Database: PDB / ID: 9mi5
TitleCrystal structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum in complex with inhibitor BKI-1606
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: 2.75 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 BKI-1606.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,1724
Polymers56,7101
Non-polymers4623
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)60.657, 55.591, 81.056
Angle α, β, γ (deg.)90.00, 104.72, 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-A1BLC / (3P)-5-amino-3-(7-ethoxyquinolin-3-yl)-1-(oxan-4-yl)-1H-pyrazole-4-carboxamide


Mass: 381.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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: 47.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.20 M Ammonium tartrate dibasic. CrpaA.01010.b.GT4.PW39259 at 16.8 mg/mL. 2mM inhibitor added prior to crystallization. plate Liu-S-165, well G5, Puck: PSL0115, Cryo: 35% PEG ...Details: 25% PEG 3350, 0.20 M Ammonium tartrate dibasic. CrpaA.01010.b.GT4.PW39259 at 16.8 mg/mL. 2mM inhibitor added prior to crystallization. plate Liu-S-165, well G5, Puck: PSL0115, Cryo: 35% PEG 3350, 0.20 M Ammonium tartrate dibasic.

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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: Nov 16, 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: 2.75→58.67 Å / Num. obs: 13118 / % possible obs: 95 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.079 / Rrim(I) all: 0.208 / Χ2: 1.12 / Net I/σ(I): 9.6 / Num. measured all: 88908
Reflection shellResolution: 2.75→2.82 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.51 / Num. measured all: 7080 / Num. unique obs: 993 / CC1/2: 0.433 / Rpim(I) all: 0.605 / Rrim(I) all: 1.628 / Χ2: 1.02 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIXdev_5533refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→54.01 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 634 4.84 %
Rwork0.2124 --
obs0.2145 13098 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→54.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 30 0 3334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063401
X-RAY DIFFRACTIONf_angle_d0.7284589
X-RAY DIFFRACTIONf_dihedral_angle_d19.2321258
X-RAY DIFFRACTIONf_chiral_restr0.042517
X-RAY DIFFRACTIONf_plane_restr0.006585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.36621390.30572577X-RAY DIFFRACTION100
2.96-3.260.34511340.26522605X-RAY DIFFRACTION100
3.26-3.730.28951060.22752115X-RAY DIFFRACTION81
3.73-4.70.22891120.16932493X-RAY DIFFRACTION94
4.7-54.010.20891430.19592674X-RAY DIFFRACTION100
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)
13.0628-0.3435-0.4941.3966-0.95191.2616-0.20650.3424-0.30460.05320.0680.0881-0.0370.64150.06260.3525-0.10720.11040.3654-0.05960.46338.502813.24284.7708
22.75380.9315-0.61590.6247-0.50751.85430.01680.04580.17720.1497-0.0694-0.0782-0.1407-0.02250.06660.2935-0.0091-0.01230.24730.02230.497521.232111.096810.2248
32.05030.01410.5443.21780.19982.0336-0.12770.59130.381-0.50410.12811.28980.07-0.29810.02330.375-0.0423-0.0890.44150.00220.69480.60016.16745.1644
41.70520.19860.12421.5647-0.32041.7029-0.0635-0.4101-0.20810.2828-0.1079-0.06450.07840.19750.1640.4656-0.03150.07710.42110.02530.413318.88322.32625.0787
51.1596-0.3601-0.23261.17110.41781.64560.2553-0.6214-0.07450.3943-0.0845-0.4555-0.03710.1398-0.14050.506-0.0076-0.06130.6260.06320.492333.73298.298231.1971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 302 )
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 391 )
5X-RAY DIFFRACTION5chain 'A' and (resid 392 through 532 )

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