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- PDB-3hko: Crystal structure of a cdpk kinase domain from cryptosporidium Pa... -

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Basic information

Entry
Database: PDB / ID: 3hko
TitleCrystal structure of a cdpk kinase domain from cryptosporidium Parvum, cgd7_40
ComponentsCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands
KeywordsTRANSFERASE / structural genomics / protist parasite / cryptosporidium parvum / cdpk / zinc finger / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Calcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Wasney, G. / Vedadi, M. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. ...Wernimont, A.K. / Hutchinson, A. / Wasney, G. / Vedadi, M. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Botchkarev, A. / Hui, R. / Artz, J.D. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of a cdpk kinase domain from cryptosporidium Parvum, cgd7_40
Authors: Wernimont, A.K. / Hutchinson, A. / Wasney, G. / Vedadi, M. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Botchkarev, A. / Hui, R. / Amani, M.
History
DepositionMay 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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 2 calmodulin-like EF hands
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2855
Polymers39,5971
Non-polymers6884
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.480, 63.045, 84.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Calcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands


Mass: 39597.469 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd7_40 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CZ29

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.82 Å3/Da / Density % sol: 32.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 25% PEG 3350, 0.2 M NaCl, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→50.44 Å / Num. all: 27579 / Num. obs: 27359 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 24.449 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.067 / Χ2: 1.007 / Net I/σ(I): 20.543
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.53 / Num. unique all: 2491 / Rsym value: 0.512 / Χ2: 0.819 / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MacCHESSdata collection
PHASERphasing
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3dfa, modified by ffas03

3dfa


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.831 / SU B: 3.217 / SU ML: 0.1 / SU R Cruickshank DPI: 0.161 / SU Rfree: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1376 5 %RANDOM
Rwork0.201 ---
all0.204 27623 --
obs0.204 27292 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.85 Å2 / Biso mean: 26.951 Å2 / Biso min: 12.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--1.39 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 39 123 2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222725
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9973711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86323.802121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67615486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4791518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212016
X-RAY DIFFRACTIONr_mcbond_it0.6351.51628
X-RAY DIFFRACTIONr_mcangle_it1.23822631
X-RAY DIFFRACTIONr_scbond_it1.81931097
X-RAY DIFFRACTIONr_scangle_it3.094.51066
LS refinement shellResolution: 1.8→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 96 -
Rwork0.276 1657 -
all-1753 -
obs--87 %

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