[English] 日本語
Yorodumi
- PDB-7fgy: Toxoplasma gondii dihydrofolate reductase thymidylate synthase (T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fgy
TitleToxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P40, 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 / 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-4TS / 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: 2.67 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)281,18116
Polymers275,3714
Non-polymers5,81012
Water6,539363
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5908
Polymers137,6852
Non-polymers2,9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-66 kcal/mol
Surface area45360 Å2
MethodPISA
2
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5908
Polymers137,6852
Non-polymers2,9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-59 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.125, 100.713, 106.036
Angle α, β, γ (deg.)85.540, 83.520, 84.670
Int Tables number1
Space group name H-MP1
Space group name HallP1

-
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


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-4TS / 5-(3-chlorophenyl)-6-[2-(3-phenoxypropoxy)ethyl]pyrimidine-2,4-diamine


Mass: 398.886 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H23ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


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


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %
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, 2.5% Benzamidine HCl

-
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 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 77348 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 40.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.274 / Num. unique obs: 7612

-
Processing

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

4eil


Resolution: 2.67→41.04 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.6253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 3485 5.05 %
Rwork0.1662 65593 -
obs0.1694 69078 85.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.55 Å2
Refinement stepCycle: LAST / Resolution: 2.67→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17881 0 384 363 18628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009718721
X-RAY DIFFRACTIONf_angle_d1.078925395
X-RAY DIFFRACTIONf_chiral_restr0.05512735
X-RAY DIFFRACTIONf_plane_restr0.00923279
X-RAY DIFFRACTIONf_dihedral_angle_d16.98396983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.710.2798480.2134885X-RAY DIFFRACTION28.76
2.71-2.750.2931820.20481753X-RAY DIFFRACTION57.2
2.75-2.790.2958940.21171888X-RAY DIFFRACTION59.99
2.79-2.830.3236880.21291952X-RAY DIFFRACTION64.15
2.83-2.880.3222970.212168X-RAY DIFFRACTION68.66
2.88-2.930.26931140.21442227X-RAY DIFFRACTION71.72
2.93-2.980.2741160.21512356X-RAY DIFFRACTION77.23
2.98-3.040.26511510.22092520X-RAY DIFFRACTION80.6
3.04-3.10.2991370.22612580X-RAY DIFFRACTION85.12
3.1-3.170.31821300.22412826X-RAY DIFFRACTION89.93
3.17-3.240.28851690.20382863X-RAY DIFFRACTION94.1
3.24-3.320.28811670.19412951X-RAY DIFFRACTION95.97
3.32-3.410.23671310.18242974X-RAY DIFFRACTION96.88
3.41-3.510.25441740.17993038X-RAY DIFFRACTION96.86
3.51-3.630.23171570.17352946X-RAY DIFFRACTION97.27
3.63-3.750.23491630.17152985X-RAY DIFFRACTION96.98
3.75-3.90.2361560.16143020X-RAY DIFFRACTION96.13
3.9-4.080.22521870.15292900X-RAY DIFFRACTION96.08
4.08-4.30.19121580.13852951X-RAY DIFFRACTION96.31
4.3-4.570.19131550.12942916X-RAY DIFFRACTION94.38
4.57-4.920.17641720.13312919X-RAY DIFFRACTION94.93
4.92-5.410.2041670.14642936X-RAY DIFFRACTION95.59
5.41-6.190.2311550.1583047X-RAY DIFFRACTION98.98
6.19-7.790.1961700.15113086X-RAY DIFFRACTION99.18
7.8-41.040.14681470.12652906X-RAY DIFFRACTION94.67

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more