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- PDB-2wwh: Plasmodium falciparum thymidylate kinase in complex with AP5dT -

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Basic information

Entry
Database: PDB / ID: 2wwh
TitlePlasmodium falciparum thymidylate kinase in complex with AP5dT
ComponentsTHYMIDILATE KINASE, PUTATIVE
KeywordsTRANSFERASE / MALARIA
Function / homology
Function and homology information


T2-induced deoxynucleotide kinase activity / guanylate kinase / dUDP biosynthetic process / guanylate kinase activity / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process ...T2-induced deoxynucleotide kinase activity / guanylate kinase / dUDP biosynthetic process / guanylate kinase activity / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWhittingham, J.L. / Carrero-Lerida, J. / Brannigan, J.A. / Ruiz-Perez, L.M. / Silva, A.P.G. / Fogg, M.J. / Wilkinson, A.J. / Gilbert, I.H. / Wilson, K.S. / Gonzalez-Pacanowska, D.
CitationJournal: Biochem.J. / Year: 2010
Title: Structural Basis for the Efficient Phosphorylation of Aztmp and Dgmp by Plasmodium Falciparum Type I Thymidylate Kinase.
Authors: Whittingham, J.L. / Carrero-Lerida, J. / Brannigan, J.A. / Ruiz-Perez, L.M. / Silva, A.P.G. / Fogg, M.J. / Wilkinson, A.J. / Gilbert, I.H. / Wilson, K.S. / Gonzalez-Pacanowska, D.
History
DepositionOct 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: THYMIDILATE KINASE, PUTATIVE
B: THYMIDILATE KINASE, PUTATIVE
C: THYMIDILATE KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,64011
Polymers74,8513
Non-polymers2,7898
Water1,802100
1
B: THYMIDILATE KINASE, PUTATIVE
C: THYMIDILATE KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7527
Polymers49,9012
Non-polymers1,8525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-49.3 kcal/mol
Surface area19110 Å2
MethodPISA
2
A: THYMIDILATE KINASE, PUTATIVE
hetero molecules

A: THYMIDILATE KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7758
Polymers49,9012
Non-polymers1,8756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2010 Å2
ΔGint-60 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.539, 109.539, 119.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2014-

HOH

21C-2014-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.318, 0.948, -0.019), (0.948, -0.318, -0.025), (-0.03, -0.01, -0.999)54.65361, -31.59403, -29.63236
2given(0.644, 0.764, -0.035), (-0.764, 0.645, 0.025), (0.041, 0.011, 0.999)54.53309, -31.7573, -29.05666

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Components

#1: Protein THYMIDILATE KINASE, PUTATIVE


Mass: 24950.326 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I4S1, dTMP kinase
#2: Chemical ChemComp-T5A / P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE


Mass: 891.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H30N7O23P5
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.98 Å3/Da / Density % sol: 58.6 % / Description: TMP-ADP COMPLEX USED AS STARTING MODEL
Crystal growpH: 7 / Details: 2.04 M SODIUM MALONATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 23265 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WWF

2wwf


Resolution: 2.7→94.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.876 / SU B: 13.024 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.971 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1189 5.2 %RANDOM
Rwork0.187 ---
obs0.191 21882 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.57 Å20 Å2
2--1.14 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.7→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 0 170 100 5509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9777348
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7735626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86324.747257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58115906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.381520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214049
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.53129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27925050
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.82532274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0544.52298
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 83 -
Rwork0.277 1437 -
obs--90.21 %

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