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- PDB-9d8s: Crystal Structure of calcium-dependent protein kinase 1 (CDPK1) f... -

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Basic information

Entry
Database: PDB / ID: 9d8s
TitleCrystal Structure of calcium-dependent protein kinase 1 (CDPK1) from Cryptosporidium parvum (AMP/Mg bound)
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
ADENOSINE MONOPHOSPHATE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsSeattle 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 (AMP/Mg bound)
Authors: Liu, L. / Cooper, A. / Lovell, S. / Battaile, K.P.
History
DepositionAug 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: 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)57,2227
Polymers56,7101
Non-polymers5116
Water1,02757
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)59.746, 55.746, 81.954
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% (w/v) PEG3350, 0.2M diammonium tartrate. CrpaA.01010.b.GT4.PW39259 at 15 mg/mL. Cocrystallized with 5mM AMP, 4mM MgCl2 and 2mM CaCl2. Plate: Liu-S-131 A10, Puck: PSL-1109, Cryo: 20% (v/v) ...Details: 25% (w/v) PEG3350, 0.2M diammonium tartrate. CrpaA.01010.b.GT4.PW39259 at 15 mg/mL. Cocrystallized with 5mM AMP, 4mM MgCl2 and 2mM CaCl2. Plate: Liu-S-131 A10, Puck: PSL-1109, Cryo: 20% (v/v) PEG 200 + 80% (w/v) crystallant

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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: Aug 3, 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: 2.12→78.92 Å / Num. obs: 29675 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.041 / Rrim(I) all: 0.092 / Χ2: 0.94 / Net I/σ(I): 9.9 / Num. measured all: 145293
Reflection shellResolution: 2.12→2.18 Å / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.989 / Num. measured all: 10505 / Num. unique obs: 2147 / CC1/2: 0.633 / Rpim(I) all: 0.491 / Rrim(I) all: 1.107 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→57.53 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1450 4.89 %
Rwork0.2086 --
obs0.2103 29638 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→57.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 28 57 3350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063355
X-RAY DIFFRACTIONf_angle_d0.7894532
X-RAY DIFFRACTIONf_dihedral_angle_d12.1591245
X-RAY DIFFRACTIONf_chiral_restr0.044515
X-RAY DIFFRACTIONf_plane_restr0.006573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.20.30961490.28542792X-RAY DIFFRACTION100
2.2-2.280.31431380.26082808X-RAY DIFFRACTION100
2.28-2.390.27511420.23532786X-RAY DIFFRACTION100
2.39-2.510.31291610.26042771X-RAY DIFFRACTION100
2.51-2.670.27741380.232822X-RAY DIFFRACTION100
2.67-2.880.27111220.21242831X-RAY DIFFRACTION100
2.88-3.170.26121540.21472827X-RAY DIFFRACTION100
3.17-3.620.25371380.20642821X-RAY DIFFRACTION100
3.63-4.570.20591610.17222832X-RAY DIFFRACTION99
4.57-57.530.2211470.2092898X-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)
11.96140.53470.25530.9386-0.29910.6865-0.15810.6611-0.6291-0.1765-0.0226-0.04490.12530.60210.01040.3187-0.05070.10170.5337-0.05290.396936.354412.03774.6473
20.2894-0.05630.09480.3298-0.49920.72880.1053-0.14190.20360.2931-0.08210.0799-0.26720.1873-00.3658-0.05820.01680.33390.02420.485926.959518.400711.2401
32.14960.6096-0.05190.78380.39221.00630.12560.0035-0.03010.0448-0.0666-0.0610.07480.01670.00010.32210.0078-0.01860.27530.0110.310917.91526.44379.6313
40.4902-0.28230.01340.62680.19690.32870.01340.1550.0409-0.34810.0059-0.04410.0007-0.13860.00010.3919-0.01630.00970.420.01670.40975.143710.25695.2516
51.35060.55320.01892.34230.49170.16460.0651-0.0352-0.071-0.0918-0.14880.53960.1581-0.50360.00010.3503-0.0017-0.03770.447-0.00830.4767-2.85113.40786.5355
60.1480.078-0.13630.5162-0.91621.6095-0.1363-0.0045-0.1327-0.0082-0.0112-0.09620.07150.057900.5184-0.02290.04790.3140.01320.363119.3286-1.80530.2719
74.0411-0.6875-1.86750.13060.42591.7104-0.00620.6907-0.57440.4737-0.4043-0.76220.24930.5024-0.99660.59-0.0422-0.1260.60680.19110.463932.03295.220726.0696
81.1301-0.4444-1.10190.18620.41971.09430.0017-0.07160.04920.3127-0.0276-0.1393-0.0736-0.3204-00.6887-0.0939-0.04340.41870.00880.407121.25042.992439.4574
90.1967-0.2021-0.370.69460.68630.8846-0.1747-1.2837-0.00330.32070.0032-0.36190.46290.9556-0.03680.37550.0336-0.04980.68180.09170.57342.10049.326924.8331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 229 )
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 269 )
5X-RAY DIFFRACTION5chain 'A' and (resid 270 through 322 )
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 360 )
7X-RAY DIFFRACTION7chain 'A' and (resid 361 through 392 )
8X-RAY DIFFRACTION8chain 'A' and (resid 393 through 451 )
9X-RAY DIFFRACTION9chain 'A' and (resid 452 through 532 )

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