[English] 日本語
Yorodumi
- PDB-5fct: Mouse thymidylate synthase in ternary complex with FdUMP and meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fct
TitleMouse thymidylate synthase in ternary complex with FdUMP and methylenetetrahydrofolate.
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Complex / Enzyme / Inhibitor / Cofactor
Function / homology
Function and homology information


response to organophosphorus / Interconversion of nucleotide di- and triphosphates / uracil metabolic process / intestinal epithelial cell maturation / response to folic acid / thymidylate synthase / sequence-specific mRNA binding / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity ...response to organophosphorus / Interconversion of nucleotide di- and triphosphates / uracil metabolic process / intestinal epithelial cell maturation / response to folic acid / thymidylate synthase / sequence-specific mRNA binding / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / cartilage development / dTMP biosynthetic process / dTTP biosynthetic process / developmental growth / response to glucocorticoid / response to cytokine / mRNA regulatory element binding translation repressor activity / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytoplasm
Similarity search - Function
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDowiercial, A. / Wilk, P. / Jarmula, A. / Rode, W.
CitationJournal: Struct Chem / Year: 2016
Title: Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme
Authors: Dowiercial, A. / Jarmula, A. / Wilk, P. / Rypniewski, W. / Kowalska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5736
Polymers70,0022
Non-polymers1,5714
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-29 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.224, 83.302, 68.850
Angle α, β, γ (deg.)90.00, 105.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Thymidylate synthase / Thymidylate synthase / isoform CRA_b


Mass: 35001.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tyms, mCG_11630 / Production host: Escherichia coli (E. coli) / References: UniProt: Q544L2, UniProt: P07607*PLUS
#2: Chemical ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12FN2O8P / Comment: inhibitor*YM
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: MES, PEG 8K, MgAcetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5406 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.55→26.14 Å / Num. obs: 85416 / % possible obs: 99.97 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
CrysalisProdata reduction
CrysalisProdata scaling
CrysalisProphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EZ8

4ez8


Resolution: 1.55→26.14 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.151 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16614 4277 5 %RANDOM
Rwork0.11726 ---
obs0.11972 81162 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.55→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 108 661 5407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195213
X-RAY DIFFRACTIONr_bond_other_d0.0010.024923
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9947097
X-RAY DIFFRACTIONr_angle_other_deg0.775311390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03923.896249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35915923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8981536
X-RAY DIFFRACTIONr_chiral_restr0.080.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021255
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_it1.4921.442435
X-RAY DIFFRACTIONr_mcbond_other1.4931.4382431
X-RAY DIFFRACTIONr_mcangle_it1.9142.1683073
X-RAY DIFFRACTIONr_mcangle_other1.9142.1683072
X-RAY DIFFRACTIONr_scbond_it2.4591.7712778
X-RAY DIFFRACTIONr_scbond_other2.4581.7712779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8832.5264006
X-RAY DIFFRACTIONr_long_range_B_refined3.88513.8236514
X-RAY DIFFRACTIONr_long_range_B_other3.22212.6546119
X-RAY DIFFRACTIONr_rigid_bond_restr1.841310136
X-RAY DIFFRACTIONr_sphericity_free27.5625170
X-RAY DIFFRACTIONr_sphericity_bonded9.844510464
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 291 -
Rwork0.213 5988 -
obs--99.97 %

+
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