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- PDB-7fgx: Toxoplasma gondii dihydrofolate reductase thymidylate synthase (T... -

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Basic information

Entry
Database: PDB / ID: 7fgx
TitleToxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P39, NADPH and dUMP
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / Toxoplasma gondii / dihydrofolate reductase / thymidylate synthase / antifolate
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
6-hexyl-5-phenyl-pyrimidine-2,4-diamine / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S.
Funding support Thailand, 1items
OrganizationGrant numberCountry
The Thailand Research Fund (TRF)TRG5780138 Thailand
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase.
Authors: Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Pengon, J. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S.
History
DepositionJul 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,66716
Polymers275,3714
Non-polymers5,29612
Water19,4741081
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3338
Polymers137,6852
Non-polymers2,6486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-65 kcal/mol
Surface area46340 Å2
MethodPISA
2
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3338
Polymers137,6852
Non-polymers2,6486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-65 kcal/mol
Surface area46430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.404, 102.536, 106.198
Angle α, β, γ (deg.)88.950, 87.740, 84.690
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
Bifunctional dihydrofolate reductase-thymidylate synthase / DHFR-TS


Mass: 68842.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-4RI / 6-hexyl-5-phenyl-pyrimidine-2,4-diamine


Mass: 270.373 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H22N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1081 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium nitrate, 14% (w/v) PEG4000 and 0.1 M Bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30.065 Å / Num. obs: 170447 / % possible obs: 95.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.4
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.407 / Num. unique obs: 16489

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
PHASER1.20.1_4487phasing
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIL

4eil


Resolution: 2.05→30.05 Å / SU ML: 0.2404 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.4972
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 8538 5.02 %
Rwork0.1804 161373 -
obs0.1821 169911 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.22 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17895 0 352 1081 19328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008318699
X-RAY DIFFRACTIONf_angle_d0.985825362
X-RAY DIFFRACTIONf_chiral_restr0.05562736
X-RAY DIFFRACTIONf_plane_restr0.00843275
X-RAY DIFFRACTIONf_dihedral_angle_d15.37976978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.35072100.33613994X-RAY DIFFRACTION69.82
2.08-2.10.35722660.30785260X-RAY DIFFRACTION92.5
2.1-2.130.31122750.27465392X-RAY DIFFRACTION94.92
2.13-2.150.30283030.26185343X-RAY DIFFRACTION94.81
2.15-2.180.292970.24895439X-RAY DIFFRACTION95.47
2.18-2.210.29992880.24035464X-RAY DIFFRACTION95.8
2.21-2.240.3192430.26265307X-RAY DIFFRACTION93.86
2.24-2.280.30252800.26625173X-RAY DIFFRACTION91.22
2.28-2.310.25682940.21345416X-RAY DIFFRACTION95.93
2.31-2.350.28162770.20985516X-RAY DIFFRACTION96.2
2.35-2.390.26533000.20615413X-RAY DIFFRACTION96.39
2.39-2.430.25053070.19945487X-RAY DIFFRACTION96.44
2.43-2.480.25622700.19765450X-RAY DIFFRACTION96.1
2.48-2.530.22172810.19335525X-RAY DIFFRACTION96.49
2.53-2.590.27472930.19575425X-RAY DIFFRACTION96.6
2.59-2.650.24823050.19455444X-RAY DIFFRACTION95.96
2.65-2.710.2352630.21085310X-RAY DIFFRACTION93.51
2.71-2.790.23653220.18695466X-RAY DIFFRACTION96.77
2.79-2.870.23812950.19015523X-RAY DIFFRACTION96.82
2.87-2.960.22232600.18935476X-RAY DIFFRACTION96.58
2.96-3.070.2442780.18645474X-RAY DIFFRACTION96.64
3.07-3.190.223000.18495499X-RAY DIFFRACTION96.51
3.19-3.330.21132890.17795447X-RAY DIFFRACTION96.63
3.33-3.510.20813160.16985362X-RAY DIFFRACTION95.01
3.51-3.730.18472860.16745434X-RAY DIFFRACTION95.8
3.73-4.020.18652710.1575458X-RAY DIFFRACTION94.93
4.02-4.420.16082760.1395478X-RAY DIFFRACTION96.37
4.42-5.060.16352820.13485414X-RAY DIFFRACTION95.94
5.06-6.360.18753130.16735480X-RAY DIFFRACTION96.76
6.36-30.050.16822980.15475504X-RAY DIFFRACTION97.14

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