1Y42	Ligase	date	Nov 29, 2004
title	Crystal Structure Of A C-Terminally Truncated Cyt-18 Protein
authors	P.J.Paukstelis, R.Coon, L.Madabusi, J.Nowakowski, A.Monzingo, J.R A.M.Lambowitz
compound		source
Molecule: Tyrosyl-Trna Synthetase, Mitochondrial Chain: X Fragment: Nucleotide-Binding Fold, Alpha Helical Domain Synonym: Tyrosine--Trna Ligase, Tyrrs Ec: 6.1.1.1 Engineered: Yes		Organism_scientific: Neurospora Crassa Organism_taxid: 5141 Gene: Cyt-18 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pex-602
symmetry	Space Group: C 1 2 1	R_factor 0.174 R_Free 0.235
crystal cell	length a length b length c angle alpha angle beta angle gamma 104.880 73.210 56.790 90.00 111.35 90.00
method	X-Ray Diffraction	resolution	1.95 Å
ligand	TYR	enzyme	Ligase E.C.6.1.1.1 BRENDA
note	1Y42 is a representative structure
Gene Ontology	Chain Function Process Component X
Primary reference	A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface., Paukstelis PJ, Coon R, Madabusi L, Nowakowski J, Monzingo A, Robertus J, Lambowitz AM, Mol Cell. 2005 Feb 4;17(3):417-28. PMID:15694342

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk] Biological Unit Coordinates (1y42.pdb1.gz) 245 Kb LPC: Ligand-Protein Contacts for 1Y42 CSU: Contacts of Structural Units for 1Y42 Likely Quarternary Molecular Structure file(s) for 1Y42 Structure Factors (393 Kb) Retrieve 1Y42 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Y42 from S2C, [Save to disk] Re-refined 1y42 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1Y42 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 1Y42

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 1Y42, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1y42] [1y42_X] SWISS-PROT database: [P12063] Domain organization of [SYYM_NEUCR] by SWISSPFAM

Other resources with information on 1Y42

Community annotation for 1Y42 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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