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- PDB-3irm: Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase CO... -

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Basic information

Entry
Database: PDB / ID: 3irm
TitleTrypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase COMPLEXED WITH Cycloguanil
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/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / 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/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, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1CY / ACETATE ION / PHOSPHATE ION / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Sep 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)237,95124
Polymers235,7124
Non-polymers2,23920
Water11,764653
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,09414
Polymers117,8562
Non-polymers1,23812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-47 kcal/mol
Surface area43890 Å2
MethodPISA
2
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,85810
Polymers117,8562
Non-polymers1,0018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-44 kcal/mol
Surface area43010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.436, 165.792, 84.767
Angle α, β, γ (deg.)90.000, 113.395, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical
ChemComp-1CY / 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine / Cycloguanil / Cycloguanil


Mass: 251.715 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14ClN5 / Comment: inhibitor, antagonist*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 44.8 %
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→29.97 Å / Num. obs: 109675 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 31 Å2 / Limit h max: 35 / Limit h min: -38 / Limit k max: 78 / Limit k min: -38 / Limit l max: 37 / Limit l min: 0 / Observed criterion F max: 2584695.41 / Observed criterion F min: 19.3 / Rsym value: 0.103 / Χ2: 0.887 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Num. unique all: 9560 / Rsym value: 0.408 / Χ2: 0.521 / % possible all: 79.8

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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 partially refined structure of 3INV

3inv


Resolution: 2.1→29.97 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5504 5 %random
Rwork0.202 ---
all-119875 --
obs-109675 91.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 51.5073 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 90.27 Å2 / Biso mean: 34.07 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å21.03 Å2
2--1.25 Å20 Å2
3---1.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16462 0 140 653 17255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg24
X-RAY DIFFRACTIONx_torsion_impr_deg0.81
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 (%)
2.1-2.20.2915704.80.243112240.012149471179478.9
2.2-2.310.275774.80.226114440.011149751202180.3
2.31-2.460.2886505.20.232117760.011149731242683
2.46-2.650.27268650.223130060.01149901369291.3
2.65-2.910.2697224.90.22140260.01150021474898.3
2.91-3.330.2818075.40.214141150.01149471492299.8
3.33-4.20.2187575.10.185142270.008150301498499.7
4.2-29.970.2097354.90.178143550.008151241509099.8

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