3VQV	Ligase	date	Apr 01, 2012
title	Crystal Structure Of The Catalytic Domain Of Pyrrolysyl-Trna Synthetase In Complex With Amppnp (Re-Refined)
authors	T.Yanagisawa, T.Sumida, R.Ishii, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Pyrrolysine--Trna Ligase Chain: A Synonym: Pyrrolysyl-Trna Synthetase, Pylrs Ec: 6.1.1.26 Engineered: Yes Mutation: Yes		Organism_scientific: Methanosarcina Mazei Organism_taxid: 2209 Strain: Jcm9314 Gene: Pyls Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Codon Plus Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28c
symmetry	Space Group: P 64	R_factor 0.187 R_Free 0.219
crystal cell	length a length b length c angle alpha angle beta angle gamma 104.876 104.876 70.433 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	ANP, MG	enzyme	Ligase E.C.6.1.1.26 BRENDA
note	3VQV supersedes 2ZCD
Gene Ontology	Chain Function Process Component A
Primary reference	A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site., Yanagisawa T, Sumida T, Ishii R, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):5-15. doi:, 10.1107/S0907444912039881. Epub 2012 Dec 20. PMID:23275158

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk] Biological Unit Coordinates (3vqv.pdb1.gz) 95 Kb LPC: Ligand-Protein Contacts for 3VQV CSU: Contacts of Structural Units for 3VQV Structure Factors (1269 Kb) Retrieve 3VQV in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3VQV from S2C, [Save to disk] Re-refined 3vqv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3VQV 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 3VQV

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 3VQV, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3vqv] [3vqv_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3VQV

Community annotation for 3VQV at PDBWiki (http://pdbwiki.org)

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