2DUL Transferase date Jul 24, 2006
title Crystal Structure Of Trna G26 Methyltransferase Trm1 In Apo Pyrococcus Horikoshii
authors Ihsanawati, M.Shirouzu, Y.Bessho, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: N(2),N(2)-Dimethylguanosine Trna Methyltransferas
Chain: A
Fragment: Residues 1-378
Synonym: Trna(Guanine-26,N(2)-N(2)) Methyltransferase, Trna Dimethylguanosine-26 Methyltransferase, Trna(M(2,2)G26) Dimethyltransferase;
Ec: 2.1.1.32
Engineered: Yes
Mutation: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Gene: Trm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus (De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: C 2 2 21
R_factor 0.195 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.909 109.662 96.676 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL enzyme Transferase E.C.2.1.1.32 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii., Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S, J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:18789948
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (2dul.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (2dul.pdb2.gz) 128 Kb
  • LPC: Ligand-Protein Contacts for 2DUL
  • CSU: Contacts of Structural Units for 2DUL
  • Likely Quarternary Molecular Structure file(s) for 2DUL
  • Structure Factors (279 Kb)
  • Retrieve 2DUL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DUL from S2C, [Save to disk]
  • Re-refined 2dul structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DUL 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 2DUL
  • 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 2DUL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dul_A] [2dul]
  • SWISS-PROT database: [O59493]
  • Domain organization of [TRM1_PYRHO] by SWISSPFAM
  • Other resources with information on 2DUL
  • Community annotation for 2DUL 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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