2YTZ	Transferase	date	Apr 05, 2007
title	Complex Structure Of Trm1 From Pyrococcus Horikoshii With S- L-Homocystein In The Orthorhombic Crystal-Lattice
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, B 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: P 21 21 2	R_factor 0.190 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 82.684 189.960 66.894 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	SAH, SO4	enzyme	Transferase E.C.2.1.1.32 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Crystal 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] (129 Kb) [Save to disk] Biological Unit Coordinates (2ytz.pdb1.gz) 64 Kb Biological Unit Coordinates (2ytz.pdb2.gz) 63 Kb Biological Unit Coordinates (2ytz.pdb3.gz) 124 Kb LPC: Ligand-Protein Contacts for 2YTZ CSU: Contacts of Structural Units for 2YTZ Likely Quarternary Molecular Structure file(s) for 2YTZ Structure Factors (259 Kb) Retrieve 2YTZ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2YTZ from S2C, [Save to disk] Re-refined 2ytz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2YTZ 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 2YTZ

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 2YTZ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ytz_B] [2ytz_A] [2ytz] SWISS-PROT database: [O59493] Domain organization of [TRM1_PYRHO] by SWISSPFAM

Other resources with information on 2YTZ

Community annotation for 2YTZ at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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