3A5Z	Ligase	date	Aug 17, 2009
title	Crystal Structure Of Escherichia Coli Genx In Complex With E Factor P
authors	T.Sumida, T.Yanagisawa, R.Ishii, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Putative Lysyl-Trna Synthetase Chain: A, C, E, G Synonym: Genx Ec: 6.1.1.6 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Strain: Mc4100 Gene: Genx, Ecs5136 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28c
Molecule: Elongation Factor P Chain: B, D, F, H Synonym: Ef-P Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Efp, Ecs5128 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28c
symmetry	Space Group: P 1 21 1	R_factor 0.226 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 105.930 102.960 119.940 90.00 99.40 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	KAA	enzyme	Ligase E.C.6.1.1.6 BRENDA
Gene Ontology	Chain Function Process Component A, E, C, G F, B, H, D
Primary reference	A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P., Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S, Nat Struct Mol Biol. 2010 Sep;17(9):1136-43. Epub 2010 Aug 22. PMID:20729861

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (305 Kb) [Save to disk] Biological Unit Coordinates (3a5z.pdb1.gz) 157 Kb Biological Unit Coordinates (3a5z.pdb2.gz) 145 Kb LPC: Ligand-Protein Contacts for 3A5Z CSU: Contacts of Structural Units for 3A5Z Structure Factors (632 Kb) Retrieve 3A5Z in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3A5Z from S2C, [Save to disk] Re-refined 3a5z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3A5Z 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 3A5Z

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 3A5Z, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3a5z_C] [3a5z] [3a5z_G] [3a5z_E] [3a5z_F] [3a5z_D] [3a5z_B] [3a5z_A] [3a5z_H] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3A5Z: [EFP] [Elong-fact-P_C ] by SMART

Other resources with information on 3A5Z

Community annotation for 3A5Z at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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