[English] 日本語
Yorodumi
- PDB-1f4b: CRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f4b
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / E. coli thymidylate synthase
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsErlanson, D.A. / Braisted, A.C. / Raphael, D.R. / Randal, M. / Stroud, R.M. / Gordon, E. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Site-directed ligand discovery.
Authors: Erlanson, D.A. / Braisted, A.C. / Raphael, D.R. / Randal, M. / Stroud, R.M. / Gordon, E.M. / Wells, J.A.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0326
Polymers30,5601
Non-polymers4725
Water4,720262
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,06412
Polymers61,1192
Non-polymers94510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_566x,-y+1,-z+3/21
Buried area6620 Å2
ΔGint-90 kcal/mol
Surface area21190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.170, 131.170, 131.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

21A-309-

HOH

DetailsThe biological assembly is a dimer constructed from chain A and a symmetry partner generated by the two-fold

-
Components

#1: Protein THYMIDYLATE SYNTHASE /


Mass: 30559.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTHYAWT / Production host: Escherichia coli (E. coli) / Strain (production host): C2913 / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.09 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulphate, 20 mM potassium phosphate, 0.2 M EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Details: Perry, K.M., (1990) Proteins: Struct.,Funct., Genet., 8, 315.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlthymidylate synthases1drop
20.2 mMEDTA1drop
31 mMdithiothreitol1drop
420 mMpotassium phosphate1drop
51.15 mMammonium sulfate1drop
62.3 Mammonium sulfate1reservoir
70.2 mMEDTA1reservoir
81 mMdithiothreitol1reservoir
920 mMpotassium phisphate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→10 Å / Num. all: 36586 / Num. obs: 36586 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4 / Num. unique all: 3443 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 104019
Reflection shell
*PLUS
% possible obs: 91.6 %

-
Processing

Software
NameClassification
REFMACrefinement
d*TREKdata scaling
RefinementResolution: 1.75→10 Å / SU B: 2.84 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.11 / ESU R Free: 0.12 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1838 5 %random
Rwork0.198 ---
all0.2 36586 --
obs0.2 36586 96.7 %-
Displacement parametersBiso mean: 37.15 Å2
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 27 262 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_mcangle_it1.953
X-RAY DIFFRACTIONp_scbond_it1.722
X-RAY DIFFRACTIONp_scangle_it2.733
X-RAY DIFFRACTIONp_chiral_restr0.1090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor15.315
X-RAY DIFFRACTIONp_transverse_tor29.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.2 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_scbond_it1.722
X-RAY DIFFRACTIONp_mcangle_it1.953
X-RAY DIFFRACTIONp_scangle_it2.733

+
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