[English] 日本語
Yorodumi
- PDB-3ihi: Crystal structure of mouse thymidylate synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ihi
TitleCrystal structure of mouse thymidylate synthase
ComponentsThymidylate synthase
KeywordsTRANSFERASE / protein-ligand complex / methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...Interconversion of nucleotide di- and triphosphates / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / heterocyclic compound binding / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to progesterone / response to cytokine / liver regeneration / response to toxic substance / circadian rhythm / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDowiercial, A. / Jarmula, A. / Rypniewski, W.R. / Sokolowska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
Citation
Journal: 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.
#1: Journal: Pteridines / Year: 2009
Title: Crystal structures of substrate- and sulfate-bound mouse thymidylate synthase
Authors: Dowiercial, A. / Jarmula, A. / Rypniewski, W.R. / Sokolowska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 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

-
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)70,1944
Polymers70,0022
Non-polymers1922
Water6,648369
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-19.1 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.202, 87.962, 68.043
Angle α, β, γ (deg.)90.000, 97.430, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Thymidylate synthase / / TSase / TS


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 / Plasmid: pPIGDM4 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: P07607, thymidylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 278 K / Method: vapor diffusion
Details: Tris-HCl pH 8.5, PEG 4000, Li2SO4, VAPOR DIFFUSION, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2008
RadiationMonochromator: Bent germanium crystal, horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. obs: 69498 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.053 / Χ2: 1.027 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-1.973.40.61734760.937198.7
1.97-2.013.60.44534690.769199.8
2.01-2.053.60.31334830.79199.9
2.05-2.093.40.29534001.005196.9
2.09-2.143.50.26234311.011198.8
2.14-2.183.70.18635140.936199.9
2.18-2.243.70.16735170.989199.9
2.24-2.33.40.16633891.151196.9
2.3-2.373.70.12634730.94199.9
2.37-2.443.70.1135240.952199.9
2.44-2.533.70.09335110.984199.8
2.53-2.633.70.08534911.013199.9
2.63-2.753.60.07835041.16199.1
2.75-2.93.70.06634801.11199.9
2.9-3.083.70.05835061.191199.8
3.08-3.313.70.0535171.072199.8
3.31-3.643.60.04735151.174199.3
3.64-4.173.50.04434881.24198.8
4.17-5.243.60.03935011.12199.1
5.24-203.50.03733091.015191.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RTS

1rts


Resolution: 1.94→19.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.964 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1366 2 %RANDOM
Rwork0.22 ---
obs0.221 67377 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 41.367 Å2 / Biso min: 21.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 10 369 4932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224679
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.966328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34723.565230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47915809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561534
X-RAY DIFFRACTIONr_chiral_restr0.1520.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213592
X-RAY DIFFRACTIONr_mcbond_it1.3781.52795
X-RAY DIFFRACTIONr_mcangle_it2.38824507
X-RAY DIFFRACTIONr_scbond_it3.49831884
X-RAY DIFFRACTIONr_scangle_it5.2414.51821
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 101 -
Rwork0.311 4846 -
all-4947 -
obs--99.4 %

+
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