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- PDB-3iro: Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase co... -

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Basic information

Entry
Database: PDB / ID: 3iro
TitleTrypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase complexed with NADPH and Q-8 antifolate
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / TRANSFERASE / Trypanosoma cruzi / DHFR-TS antifolate complex / Methyltransferase / Multifunctional enzyme / NADP / Nucleotide biosynthesis / One-carbon metabolism
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
Chem-2CY / ACETATE ION / Chem-NDP / PHOSPHATE ION / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChitnumsub, P. / Yuvaniyama, J. / Yuthavong, Y.
CitationJournal: To be Published
Title: Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase
Authors: Chitnumsub, P. / Yuvaniyama, J. / Vilaivan, T. / Vanichtanankul, J. / Kamchonwongpaisan, S. / Yuthavong, Y.
History
DepositionAug 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,16228
Polymers235,7124
Non-polymers5,45024
Water1,49583
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,52213
Polymers117,8562
Non-polymers2,66611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-43 kcal/mol
Surface area42660 Å2
MethodPISA
2
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,64015
Polymers117,8562
Non-polymers2,78413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-44 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.544, 165.936, 84.718
Angle α, β, γ (deg.)90.000, 113.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 58928.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Y / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: Q27793, dihydrofolate reductase, thymidylate synthase

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Non-polymers , 6 types, 107 molecules

#2: Chemical
ChemComp-2CY / 5-[3-(3-fluorophenoxy)propoxy]quinazoline-2,4-diamine


Mass: 328.341 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H17FN4O2
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 297 K / Method: microbatch / pH: 5.6
Details: PEG4000, NH4OAc, pH 5.6, microbatch, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å
DetectorType: Kappa CCD / Detector: CCD / Date: Aug 30, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→45.07 Å / Num. all: 48261 / Num. obs: 48286 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 48 Å2 / Limit h max: 26 / Limit h min: -29 / Limit k max: 59 / Limit k min: -29 / Limit l max: 30 / Limit l min: 0 / Observed criterion F max: 1995264.21 / Observed criterion F min: 25.4 / Rsym value: 0.097 / Χ2: 1.472 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.9 Å / Num. unique all: 4296 / Rsym value: 0.397 / Χ2: 1.264 / % possible all: 85

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A partial refined structure of 1IRM

1irm


Resolution: 2.8→45.07 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2478 5.1 %random
Rwork0.206 ---
all-50769 --
obs-48261 95.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 23.5073 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 90.76 Å2 / Biso mean: 32.37 Å2 / Biso min: 1.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å21.38 Å2
2--0.67 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.48 Å
Luzzati d res high-2.8
Refinement stepCycle: LAST / Resolution: 2.8→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16419 0 360 83 16862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.930.372624.90.32851210.0236338538384.9
2.93-3.080.3643075.40.29353960.0216325570390.2
3.08-3.280.33929750.25856670.026335596494.1
3.28-3.530.3123175.20.23358180.0186348613596.6
3.53-3.880.2530850.19559100.0146325621898.3
3.88-4.440.2443305.30.16759540.0136334628499.2
4.44-5.60.2343275.20.15759700.0136365629798.9
5.6-45.070.2453305.30.17459470.0136427627797.7

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