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- PDB-4ysm: Calcium-Dependent Protein Kinase from Eimeria tenella -

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Basic information

Entry
Database: PDB / ID: 4ysm
TitleCalcium-Dependent Protein Kinase from Eimeria tenella
ComponentsCalmodulin-like domain protein kinase
KeywordsTRANSFERASE / serine/threonine protein kinase / calcium-binding / ATP-binding
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
Calmodulin-like domain protein kinase
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å
AuthorsMerritt, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089441 United States
CitationJournal: to be published
Title: CDPK is a druggable target in the apicomplexan parasite Eimeria
Authors: Ojo, K.K. / Vidadala, R. / Maly, D.J. / Van Voorhis, W.C. / Merritt, E.A.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-like domain protein kinase
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,65810
Polymers111,3372
Non-polymers3218
Water362
1
A: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8295
Polymers55,6691
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8295
Polymers55,6691
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.669, 109.556, 77.729
Angle α, β, γ (deg.)90.000, 92.170, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 7 - 481 / Label seq-ID: 11 - 485

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Calmodulin-like domain protein kinase


Mass: 55668.504 Da / Num. of mol.: 2 / Mutation: A410D
Source method: isolated from a genetically manipulated source
Details: cleaved N-terminal His-tag / Source: (gene. exp.) Eimeria tenella (eukaryote) / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3HNM4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THAT THE UNP REFERENCE Q3HNM4 IS INCORRECT AT RESIDUE 410. THE RESIDUE IDENTITY OF ...AUTHOR STATED THAT THE UNP REFERENCE Q3HNM4 IS INCORRECT AT RESIDUE 410. THE RESIDUE IDENTITY OF 410 SHOULD BE ASP INSTEAD OF ALA BECAUSE THIS RESIDUE IS IN BINDING TO CALCIUM AND CONSERVED ACROSS THE LARGER FAMILY OF CDPKS.

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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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: protein buffer: 25 mM HEPES pH 7.0, 5% glycerol, 500 mM NaCl, 2 mM DTT, 175 uM EtCDPK1; crystallization buffer: 100 mM BIS/TRIS pH 6.5, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.19→38.84 Å / Num. obs: 18399 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 78 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.497 / Rpim(I) all: 0.203 / Net I/σ(I): 5.6 / Num. measured all: 127487 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.19-3.416.72.99412186032800.2541.24597.9
9.03-38.846.80.05623.256878390.9970.02497.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3q5i

3q5i


Resolution: 3.19→38.84 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.2554 / WRfactor Rwork: 0.2084 / FOM work R set: 0.7306 / SU B: 81.955 / SU ML: 0.614 / SU R Cruickshank DPI: 0.496 / SU Rfree: 0.6056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.606 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 910 5 %RANDOM
Rwork0.2284 ---
obs0.2311 17298 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.04 Å2 / Biso mean: 73.509 Å2 / Biso min: 26.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å21.77 Å2
2--3.89 Å2-0 Å2
3----4.65 Å2
Refinement stepCycle: final / Resolution: 3.19→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 8 2 7528
Biso mean--73.93 35.96 -
Num. residues----950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197692
X-RAY DIFFRACTIONr_bond_other_d0.0040.027358
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.97110298
X-RAY DIFFRACTIONr_angle_other_deg0.993316964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6624.815351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.121151426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8351542
X-RAY DIFFRACTIONr_chiral_restr0.0780.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028556
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021672
X-RAY DIFFRACTIONr_mcbond_it2.5384.2063805
X-RAY DIFFRACTIONr_mcbond_other2.5374.2063804
X-RAY DIFFRACTIONr_mcangle_it4.376.3064744
Refine LS restraints NCS

Ens-ID: 1 / Number: 29127 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.194→3.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 64 -
Rwork0.35 1121 -
all-1185 -
obs--86.18 %
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)
16.21513.5861-5.13762.8912-3.67077.57520.59620.57820.30930.44150.04250.2068-0.4527-0.4053-0.63860.32260.0276-0.05080.1719-0.00320.4454-42.22215.279-37.967
20.6829-1.58730.68183.9449-0.97012.7797-0.06880.05510.16160.0518-0.0511-0.4278-0.05670.1470.11990.1481-0.0791-0.0030.0473-0.00110.489-32.6876.121-32.688
30.9411-0.89671.16731.0897-1.23861.54470.1408-0.4669-0.241-0.50160.02130.17950.4073-0.3908-0.16210.860.15010.26161.0186-0.03951.0964-37.381-11.632-35.885
42.5644-1.7602-0.65333.8878-1.64364.5598-0.25910.0344-0.0728-0.1832-0.2089-0.95490.55230.46560.4680.24920.04520.10750.07650.06110.799-19.676-12.961-28.39
50.53550.0055-0.38071.73351.58161.8712-0.1633-0.0742-0.14050.50190.055-0.12450.40910.14170.10830.3758-0.012-0.08890.08390.04090.5358-38.5614.264-12.437
60.9052-0.1410.27020.10760.08176.6966-0.0260.10250.09860.0502-0.02370.1705-0.6643-0.36250.04970.28730.0260.0030.0666-0.01240.5179-55.81218.767-23.7
75.56541.807-5.96111.6855-2.59111.0747-0.17360.0345-0.1401-0.0765-0.2199-0.14590.107-0.33090.39340.1280.0057-0.10970.092-0.00890.4072-66.649-39.868-10.319
83.90641.6029-0.28223.64470.42950.42960.1732-0.0026-0.09920.4425-0.0608-0.1139-0.0151-0.0862-0.11230.2496-0.01190.00130.02260.04110.3513-61.153-30.421-2.077
94.5583-1.2350.70635.4960.59922.1112-0.03820.0953-0.01990.5609-0.04690.5884-0.0726-0.17060.08510.227-0.0110.11340.0231-0.0150.3202-59.416-20.736-1.227
104.6064-0.321-1.98253.77270.09273.0350.3412-0.38770.27320.87410.0155-0.2567-0.17920.3102-0.35670.4118-0.0571-0.06320.0507-0.07830.439-49.826-12.7697.077
116.41070.87060.53622.903-0.25571.79650.3592-0.2419-0.05770.1915-0.1844-0.2734-0.04150.1732-0.17480.16230.008-0.04720.0469-0.03730.2939-40.462-35.946-15.217
126.24870.3730.89530.76270.07471.38060.30050.3948-0.469-0.1671-0.17830.07280.284-0.0914-0.12220.20960.0504-0.06750.0969-0.06360.3958-54.101-43.168-25.529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 40
2X-RAY DIFFRACTION2A41 - 171
3X-RAY DIFFRACTION3A172 - 191
4X-RAY DIFFRACTION4A192 - 255
5X-RAY DIFFRACTION5A256 - 377
6X-RAY DIFFRACTION5A501
7X-RAY DIFFRACTION6A378 - 481
8X-RAY DIFFRACTION6A502
9X-RAY DIFFRACTION6A503
10X-RAY DIFFRACTION6A504
11X-RAY DIFFRACTION7B7 - 40
12X-RAY DIFFRACTION8B41 - 161
13X-RAY DIFFRACTION9B162 - 193
14X-RAY DIFFRACTION10B194 - 295
15X-RAY DIFFRACTION11B296 - 377
16X-RAY DIFFRACTION11B501
17X-RAY DIFFRACTION12B378 - 481
18X-RAY DIFFRACTION12B502
19X-RAY DIFFRACTION12B503
20X-RAY DIFFRACTION12B504

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