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- PDB-4eil: Crystal Structure of the loop truncated Toxoplasma gondii TS-DHFR -

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Basic information

Entry
Database: PDB / ID: 4eil
TitleCrystal Structure of the loop truncated Toxoplasma gondii TS-DHFR
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / TRANSFERASE / bifunctional
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 / mitochondrion / cytosol
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / FOLIC ACID / 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: 2.1971 Å
AuthorsSharma, H.
CitationJournal: Biochemistry / Year: 2013
Title: First Three-Dimensional Structure of Toxoplasma gondii Thymidylate Synthase-Dihydrofolate Reductase: Insights for Catalysis, Interdomain Interactions, and Substrate Channeling.
Authors: Sharma, H. / Landau, M.J. / Vargo, M.A. / Spasov, K.A. / Anderson, K.S.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

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
E: Bifunctional dihydrofolate reductase-thymidylate synthase
F: Bifunctional dihydrofolate reductase-thymidylate synthase
G: Bifunctional dihydrofolate reductase-thymidylate synthase
H: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)529,49440
Polymers513,7148
Non-polymers15,78032
Water32,9851831
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,37410
Polymers128,4292
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-58 kcal/mol
Surface area38620 Å2
MethodPISA
2
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,37410
Polymers128,4292
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-58 kcal/mol
Surface area38680 Å2
MethodPISA
3
E: Bifunctional dihydrofolate reductase-thymidylate synthase
F: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,37410
Polymers128,4292
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-60 kcal/mol
Surface area38740 Å2
MethodPISA
4
G: Bifunctional dihydrofolate reductase-thymidylate synthase
H: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,37410
Polymers128,4292
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-60 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.787, 144.399, 177.605
Angle α, β, γ (deg.)90.01, 89.93, 90.38
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 64214.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: K-12 / Gene: DRTS / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase

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Non-polymers , 5 types, 1863 molecules

#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical
ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H19N7O6
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1831 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 10mg/ml protein, PEG 3350, Potassium formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9594 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2011
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9594 Å / Relative weight: 1
ReflectionResolution: 2.197→50 Å / Num. obs: 265057 / % possible obs: 98 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.197-2.244.90.691196.3
2.24-2.285.30.66196.7
2.28-2.3260.575196.9
2.32-2.376.60.555197.1
2.37-2.426.70.517197.2
2.42-2.486.50.463197.3
2.48-2.546.90.403197.6
2.54-2.6170.358197.6
2.61-2.696.80.332197.7
2.69-2.776.90.274197.9
2.77-2.877.10.237197.9
2.87-2.996.80.206198.3
2.99-3.127.10.172198.3
3.12-3.2970.148198.5
3.29-3.496.90.128198.6
3.49-3.7670.111198.8
3.76-4.1470.116199
4.14-4.7470.143199.1
4.74-5.9770.167199.4
5.97-5070.25199.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ECK

4eck


Resolution: 2.1971→48.403 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.28 / σ(F): 1.98 / Phase error: 25.51 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.2333 13373 5.05 %
Rwork0.183 --
obs0.1855 264952 97.24 %
all-278434 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.546 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å2-0.99 Å2-0.68 Å2
2---2.49 Å2-0.03 Å2
3---5.58 Å2
Refinement stepCycle: LAST / Resolution: 2.1971→48.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32064 0 1080 1831 34975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834120
X-RAY DIFFRACTIONf_angle_d1.80846348
X-RAY DIFFRACTIONf_dihedral_angle_d16.94812600
X-RAY DIFFRACTIONf_chiral_restr0.1295036
X-RAY DIFFRACTIONf_plane_restr0.0055888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1971-2.2220.3333160.24126540X-RAY DIFFRACTION75
2.222-2.24820.2944730.23348308X-RAY DIFFRACTION97
2.2482-2.27560.3014380.22778233X-RAY DIFFRACTION97
2.2756-2.30440.27454020.21358493X-RAY DIFFRACTION97
2.3044-2.33470.28464630.2188406X-RAY DIFFRACTION97
2.3347-2.36670.29484250.21018320X-RAY DIFFRACTION97
2.3667-2.40050.28714560.21278307X-RAY DIFFRACTION97
2.4005-2.43630.30514370.21258517X-RAY DIFFRACTION97
2.4363-2.47440.26614260.20638375X-RAY DIFFRACTION97
2.4744-2.5150.284350.20618309X-RAY DIFFRACTION98
2.515-2.55830.28045030.20368520X-RAY DIFFRACTION98
2.5583-2.60490.2744490.20198304X-RAY DIFFRACTION98
2.6049-2.6550.27814540.2038417X-RAY DIFFRACTION98
2.655-2.70910.28364500.20768463X-RAY DIFFRACTION98
2.7091-2.7680.26884440.2068430X-RAY DIFFRACTION98
2.768-2.83240.2844700.20438535X-RAY DIFFRACTION98
2.8324-2.90330.25754460.19598362X-RAY DIFFRACTION98
2.9033-2.98170.26744720.20058491X-RAY DIFFRACTION98
2.9817-3.06950.26914380.20338411X-RAY DIFFRACTION98
3.0695-3.16850.2834400.2198576X-RAY DIFFRACTION98
3.1685-3.28170.28524320.20578447X-RAY DIFFRACTION99
3.2817-3.41310.24314660.20138515X-RAY DIFFRACTION99
3.4131-3.56840.24154360.18788573X-RAY DIFFRACTION99
3.5684-3.75650.22234410.188448X-RAY DIFFRACTION99
3.7565-3.99170.20574400.16298555X-RAY DIFFRACTION99
3.9917-4.29980.17424540.14488537X-RAY DIFFRACTION99
4.2998-4.73210.17064370.1438555X-RAY DIFFRACTION99
4.7321-5.41610.19814960.1528565X-RAY DIFFRACTION99
5.4161-6.82070.21084700.17458581X-RAY DIFFRACTION100
6.8207-48.41450.20034640.1768486X-RAY DIFFRACTION99

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