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- PDB-3mse: Crystal structure of C-terminal domain of PF110239. -

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Basic information

Entry
Database: PDB / ID: 3mse
TitleCrystal structure of C-terminal domain of PF110239.
ComponentsCalcium-dependent protein kinase, putative
KeywordsTRANSFERASE / cdpks / malaria / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / MAPK6/MAPK4 signaling / calcium-dependent protein serine/threonine kinase activity / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / peptidyl-serine phosphorylation / protein autophosphorylation / calmodulin binding / intracellular signal transduction ...CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / MAPK6/MAPK4 signaling / calcium-dependent protein serine/threonine kinase activity / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / peptidyl-serine phosphorylation / protein autophosphorylation / calmodulin binding / intracellular signal transduction / calcium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / 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 ...EF hand / EF-hand / Recoverin; domain 1 / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-dependent protein kinase 6
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWernimont, A.K. / Artz, J.D. / Hutchinson, A. / Sullivan, H. / Weadge, J. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Artz, J.D. / Hutchinson, A. / Sullivan, H. / Weadge, J. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Lin, Y.H. / Neculai, A.M. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of C-terminal domain of PF110239
Authors: Wernimont, A.K. / Artz, J.D. / Hutchinson, A. / Sullivan, H. / Weadge, J. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Lin, Y.H. / ...Authors: Wernimont, A.K. / Artz, J.D. / Hutchinson, A. / Sullivan, H. / Weadge, J. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Lin, Y.H. / Neculai, A.M. / Amani, M. / Structural Genomics Consortium (SGC)
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Calcium-dependent protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2605
Polymers20,9881
Non-polymers2724
Water1,04558
1
B: Calcium-dependent protein kinase, putative
hetero molecules

B: Calcium-dependent protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,52110
Polymers41,9762
Non-polymers5458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6670 Å2
ΔGint-135 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.757, 101.757, 44.895
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Calcium-dependent protein kinase, putative


Mass: 20988.006 Da / Num. of mol.: 1
Fragment: C-TERMINAL DOMAIN OF PF110239 (UNP residues 1439:1617)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF11_0239 / Plasmid: Pet15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): bl21de3 / References: UniProt: Q8IID5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 % PEG 400, 0.2 M Ammonium sulfate, 0.05 M Hepes 7.5, 2 mM AMPPNP, 4 mM CaCL2, MgCl2, 6.25 mM TCEp, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9792
SYNCHROTRONCLSI 08ID-120.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 24, 2010
MARMOSAIC 225 mm CCD2CCDSep 10, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 15890 / Num. obs: 15859 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.335 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 4.55 / Num. unique all: 804 / Χ2: 1.09 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.222 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.796 / SU B: 5.18 / SU ML: 0.137 / SU R Cruickshank DPI: 0.196 / SU Rfree: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY; Density between residues 104 and 107 is poor - unclear if domain swapped into symmetry mate.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 789 5 %RANDOM
Rwork0.222 ---
all0.224 15877 --
obs0.224 15825 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 84.87 Å2 / Biso mean: 45.38 Å2 / Biso min: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20.69 Å20 Å2
2--1.38 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 12 58 1447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221487
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9322017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4195181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51124.80577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74315272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.912157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021132
X-RAY DIFFRACTIONr_mcbond_it0.7021.5882
X-RAY DIFFRACTIONr_mcangle_it1.33121440
X-RAY DIFFRACTIONr_scbond_it1.9093605
X-RAY DIFFRACTIONr_scangle_it3.0344.5577
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 67 -
Rwork0.279 1085 -
all-1152 -
obs--99.22 %

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