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- PDB-2wwf: Plasmodium falciparum thymidylate kinase in complex with TMP and ADP -

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Basic information

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


T2-induced deoxynucleotide kinase activity / guanylate kinase / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity ...T2-induced deoxynucleotide kinase activity / guanylate kinase / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 1.1Mar 25, 2015Group: Non-polymer description / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)78,08925
Polymers74,8513
Non-polymers3,23822
Water8,809489
1
A: THYMIDILATE KINASE, PUTATIVE
hetero molecules

A: THYMIDILATE KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,09018
Polymers49,9012
Non-polymers2,18916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6620 Å2
ΔGint-100 kcal/mol
Surface area18840 Å2
MethodPISA
2
B: THYMIDILATE KINASE, PUTATIVE
C: THYMIDILATE KINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,04416
Polymers49,9012
Non-polymers2,14314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-85.4 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.127, 110.127, 120.097
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
11C-2111-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.317, 0.948, -0.008), (0.948, -0.318, -0.02), (-0.021, -0.001, -1)55.21868, -31.76627, -29.17687
2given(0.637, 0.771, -0.015), (-0.77, 0.637, 0.018), (0.024, 1)55.11794, -31.96332, -28.93552

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 511 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: NONE
Crystal growpH: 7.5
Details: 75 MM HEPES PH 7.5, 1.35 M TRI- SODIUM CITRATE, 0.125 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 67190 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 47.4

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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 1E2Q

1e2q


Resolution: 1.89→95.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.69 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3198 5 %RANDOM
Rwork0.16 ---
obs0.163 60137 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.89→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 205 489 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9817486
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29825.167269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9815935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.9891517
X-RAY DIFFRACTIONr_chiral_restr0.2240.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214130
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_it1.1441.53163
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05825124
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4532353
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3374.52359
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: 1.9→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 138 -
Rwork0.229 2340 -
obs--50.63 %

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