[English] 日本語
Yorodumi
- PDB-4eil: Crystal Structure of the loop truncated Toxoplasma gondii TS-DHFR -

+
Open data


ID or keywords:

Loading...

-
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
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: 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

-
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
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

-
Components

-
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

-
Non-polymers , 5 types, 1863 molecules

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


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 / Folate


Mass: 441.397 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1831 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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