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- PDB-1v0b: Crystal structure of the t198a mutant of pfpk5 -

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Basic information

Entry
Database: PDB / ID: 1v0b
TitleCrystal structure of the t198a mutant of pfpk5
ComponentsCELL DIVISION CONTROL PROTEIN 2 HOMOLOG
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / CDK
Function / homology
Function and homology information


[RNA-polymerase]-subunit kinase / synaptic vesicle transport / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / vesicle-mediated transport / RNA polymerase II CTD heptapeptide repeat kinase activity / axonogenesis / cell cycle / phosphorylation / cell division ...[RNA-polymerase]-subunit kinase / synaptic vesicle transport / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / vesicle-mediated transport / RNA polymerase II CTD heptapeptide repeat kinase activity / axonogenesis / cell cycle / phosphorylation / cell division / protein serine kinase activity / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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. ...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
Cyclin-dependent kinase 2 homolog
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHolton, S. / Merckx, A. / Burgess, D. / Doerig, C. / Noble, M. / Endicott, J.
CitationJournal: Structure / Year: 2003
Title: Structures of P. Falciparum Pfpk5 Test the Cdk Regulation Paradigm and Suggest Mechanisms of Small Molecule Inhibition
Authors: Holton, S. / Merckx, A. / Burgess, D. / Doerig, C. / Noble, M. / Endicott, J.
History
DepositionMar 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG
B: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)66,0262
Polymers66,0262
Non-polymers00
Water5,657314
1
A: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)33,0131
Polymers33,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)33,0131
Polymers33,0131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.290, 94.653, 133.229
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CELL DIVISION CONTROL PROTEIN 2 HOMOLOG / PFPK5


Mass: 33013.145 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q07785, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION THR 198 ALA IN CHAINS A AND B FUNCTION: PLAYS A KEY ROLE IN THE CONTROL OF THE ...ENGINEERED MUTATION THR 198 ALA IN CHAINS A AND B FUNCTION: PLAYS A KEY ROLE IN THE CONTROL OF THE EUKARYOTIC CELL CYCLE. IT IS REQUIRED IN HIGHER CELLS FOR ENTRY INTO S-PHASE AND MITOSIS.

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growpH: 7.4 / Details: pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→27 Å / Num. obs: 33495 / % possible obs: 97 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.098

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→129.1 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1679 5 %RANDOM
Rwork0.223 ---
obs0.226 31806 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å2-0.66 Å2
2---1.39 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4414 0 0 314 4728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224510
X-RAY DIFFRACTIONr_bond_other_d00.024181
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9736090
X-RAY DIFFRACTIONr_angle_other_deg3.55339762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2615543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024893
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02887
X-RAY DIFFRACTIONr_nbd_refined0.250.21109
X-RAY DIFFRACTIONr_nbd_other0.290.24638
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1080.22215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7270.262
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5730.2165
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5720.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0881.52720
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99224394
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6631790
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3764.51696
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 93
Rwork0.272 2039

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