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- PDB-4eck: Crystal Structure of the Toxoplasma gondii TS-DHFR -

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Basic information

Entry
Database: PDB / ID: 4eck
TitleCrystal Structure of the Toxoplasma gondii TS-DHFR
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
Keywordstransferase / oxidoreductase / 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
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
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: 3.516 Å
AuthorsSharma, H. / Anderson, K.S.
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
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 4, 2015Group: Structure summary
Revision 1.3Nov 15, 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 1.4Sep 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,63010
Polymers137,6852
Non-polymers3,9458
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-62 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.944, 143.015, 59.840
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 68842.656 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O6
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 290 K / Method: hanging drop / pH: 7.3
Details: PEG 3350, Potassium formate, pH 7.3, 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: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2010
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9594 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 19084 / % possible obs: 93.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.301 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
3.5-3.566.91,288.3
3.56-3.636.91,289.60.969
3.63-3.696.91,288.60.865
3.69-3.776.71,2890.793
3.77-3.856.81,290.50.884
3.85-3.946.71,289.60.888
3.94-4.046.71,290.50.622
4.04-4.156.61,293.60.581
4.15-4.276.61,293.50.492
4.27-4.416.51,295.50.334
4.41-4.576.61,296.30.319
4.57-4.756.51,297.70.289
4.75-4.976.71,298.60.291
4.97-5.236.91,297.90.267
5.23-5.556.91,298.10.276
5.55-5.986.91,297.60.266
5.98-6.586.91,295.80.252
6.58-7.536.91,288.90.168
7.53-9.4871,299.20.094
9.48-506.71,298.90.069

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZF and 3NZA

1qzf

3nza


Resolution: 3.516→46.18 Å / Cor.coef. Fo:Fc: 0.761 / Cor.coef. Fo:Fc free: 0.624 / Occupancy max: 1 / Occupancy min: 0.31 / SU B: 156.229 / SU ML: 1.107 / Cross valid method: THROUGHOUT / ESU R Free: 0.978
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.39529 982 5.2 %RANDOM
Rwork0.33184 ---
obs0.33492 17754 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.09 Å2
2--0.19 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 3.516→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7978 0 270 0 8248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.98911442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8395970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10723.196388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.006151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7261566
X-RAY DIFFRACTIONr_chiral_restr0.1020.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216360
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.516→3.607 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 124 -
Rwork0.377 1114 -
obs--87.99 %
Refinement TLS params.Method: refined / Origin x: -54.4753 Å / Origin y: -3.87 Å / Origin z: -29.913 Å
111213212223313233
T0.2136 Å20.0163 Å2-0.0013 Å2-0.2688 Å2-0.0438 Å2--0.0141 Å2
L0.3783 °20.127 °2-0.085 °2-0.9556 °2-0.3315 °2--0.3836 °2
S0.0448 Å °-0.0182 Å °-0.0221 Å °0.0194 Å °-0.0102 Å °0.0111 Å °0.0099 Å °-0.0093 Å °-0.0346 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 610
2X-RAY DIFFRACTION1A701 - 704
3X-RAY DIFFRACTION1B3 - 610
4X-RAY DIFFRACTION1B701 - 704

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