3A26 Transferase date Apr 28, 2009
title Crystal Structure Of P. Horikoshii Tyw2 In Complex With Mesa
authors M.Umitsu, H.Nishimasu, R.Ishitani, O.Nureki
compound source
Molecule: Uncharacterized Protein Ph0793
Chain: A
Synonym: Tyw2
Engineered: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Gene: Ph0793
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: H 3
R_factor 0.213 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.571 132.571 96.669 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand MTA, PG4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2., Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O, Proc Natl Acad Sci U S A. 2009 Aug 26. PMID:19717466
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3a26.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 3A26
  • CSU: Contacts of Structural Units for 3A26
  • Structure Factors (168 Kb)
  • Retrieve 3A26 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A26 from S2C, [Save to disk]
  • Re-refined 3a26 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A26 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3A26
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3A26, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a26_A] [3a26]
  • SWISS-PROT database: [O58523]
  • Domain organization of [O58523_PYRHO] by SWISSPFAM
  • Other resources with information on 3A26
  • Community annotation for 3A26 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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