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- PDB-3f3z: Crystal structure of Cryptosporidium parvum calcium dependent pro... -

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Basic information

Entry
Database: PDB / ID: 3f3z
TitleCrystal structure of Cryptosporidium parvum calcium dependent protein kinase cgd7_1840 in presence of indirubin E804
ComponentsCalcium/calmodulin-dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
KeywordsTRANSFERASE / KINASE / calcium dependent protein kinase / structural genomics consortium / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / SGC
Function / homology
Function and homology information


starch binding / calcium-dependent protein serine/threonine kinase activity / mitogen-activated protein kinase binding / calmodulin-dependent protein kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding ...starch binding / calcium-dependent protein serine/threonine kinase activity / mitogen-activated protein kinase binding / calmodulin-dependent protein kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / 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. ...Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / 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. / Immunoglobulin-like fold / 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-DRK / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsWernimont, A.K. / Lew, J. / Wasney, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. ...Wernimont, A.K. / Lew, J. / Wasney, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Cryptosporidium parvum calcium dependent protein kinase cgd7_1840 in presence of indirubin E804
Authors: Wernimont, A.K. / Lew, J. / Wasney, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D. / Amani, M.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6806
Polymers31,9471
Non-polymers7345
Water3,801211
1
A: Calcium/calmodulin-dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules

A: Calcium/calmodulin-dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,36112
Polymers63,8932
Non-polymers1,46810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5210 Å2
ΔGint-24 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.316, 82.864, 62.151
Angle α, β, γ (deg.)90.00, 111.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase with a kinase domain and 4 calmodulin like EF hands


Mass: 31946.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd7_1840 / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q5CYL9
#2: Chemical ChemComp-DRK / 3-({[(3S)-3,4-dihydroxybutyl]oxy}amino)-1H,2'H-2,3'-biindol-2'-one / Indirubin_E804


Mass: 365.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% PEG 3350, 0.1 M NH4SO4, 0.1 M NaCacodylate, 5 mM Indirubin E804, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 25859 / Num. obs: 25653 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.754 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.032 / Χ2: 1.481
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2464 / Rsym value: 0.53 / Χ2: 1.408 / % possible all: 95.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qg5

2qg5


Resolution: 1.84→57.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.859 / SU B: 2.815 / SU ML: 0.088 / SU R Cruickshank DPI: 0.145 / SU Rfree: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1303 5.1 %RANDOM
Rwork0.187 ---
all0.189 25825 --
obs0.189 25653 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.99 Å2 / Biso mean: 27.471 Å2 / Biso min: 13.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.42 Å2
2--0.57 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.84→57.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 51 211 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222303
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9993115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2785275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34123.529102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20715.037407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1561517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021712
X-RAY DIFFRACTIONr_nbd_refined0.1920.21045
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.222
X-RAY DIFFRACTIONr_mcbond_it0.8121.51413
X-RAY DIFFRACTIONr_mcangle_it1.27822219
X-RAY DIFFRACTIONr_scbond_it1.70431120
X-RAY DIFFRACTIONr_scangle_it2.7884.5894
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 112 -
Rwork0.291 1725 -
all-1837 -
obs--96.74 %

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