1VBM	Ligase	date	Feb 27, 2004
title	Crystal Structure Of The Escherichia Coli Tyrosyl-Trna Synth Complexed With Tyr-Ams
authors	T.Kobayashi, K.Sakamoto, T.Takimura, K.Kamata, R.Sekine, S.Nishim S.Yokoyama, Riken Structural Genomicsproteomics Initiative
compound		source
Molecule: Tyrosyl-Trna Synthetase Chain: A, B Fragment: Residues 5-322 Synonym: Tyrosine--Trna Ligase, Tyrrs Ec: 6.1.1.1 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-6p1
symmetry	Space Group: P 32 2 1	R_factor 0.246 R_Free 0.284
crystal cell	length a length b length c angle alpha angle beta angle gamma 83.189 83.189 182.424 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	SO4, YSA	enzyme	Ligase E.C.6.1.1.1 BRENDA
related structures	by homologous chain: 1VBN
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase., Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S, J Mol Biol. 2005 Feb 11;346(1):105-17. Epub 2004 Dec 15. PMID:15663931

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk] Biological Unit Coordinates (1vbm.pdb1.gz) 105 Kb LPC: Ligand-Protein Contacts for 1VBM CSU: Contacts of Structural Units for 1VBM Likely Quarternary Molecular Structure file(s) for 1VBM Structure Factors (264 Kb) Retrieve 1VBM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VBM from S2C, [Save to disk] Re-refined 1vbm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VBM 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 1VBM

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 1VBM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1vbm_A] [1vbm_B] [1vbm] SWISS-PROT database: [P0AGJ9] Domain organization of [SYY_ECOLI] by SWISSPFAM

Other resources with information on 1VBM

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

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