2V9D	Lyase	date	Aug 23, 2007
title	Crystal Structure Of Yage, A Prophage Protein Belonging To T Dihydrodipicolinic Acid Synthase Family From E. Coli K12
authors	S.Manicka, Y.Peleg, T.Unger, S.Albeck, O.Dym, H.M.Greenblatt, G.Bo V.Lamzin, S.Krishnaswamy, J.L.Sussman
compound		source
Molecule: Yage Chain: A, B, C, D Fragment: Residues 3-309 Synonym: Putative Lyase-Synthase Yage Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K12 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector: Pet28a Expression_system_plasmid: Pet28tevhyage Other_details: Genobase, Tokyo
symmetry	Space Group: P 1 21 1	R_factor 0.166 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 56.279 149.806 78.967 90.00 108.42 90.00
method	X-Ray Diffraction	resolution	2.15 Å
ligand	MSE	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12., Manicka S, Peleg Y, Unger T, Albeck S, Dym O, Greenblatt HM, Bourenkov G, Lamzin V, Krishnaswamy S, Sussman JL, Proteins. 2008 Jun;71(4):2102-8. PMID:18361457

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (200 Kb) [Save to disk] Biological Unit Coordinates (2v9d.pdb1.gz) 193 Kb LPC: Ligand-Protein Contacts for 2V9D CSU: Contacts of Structural Units for 2V9D Likely Quarternary Molecular Structure file(s) for 2V9D Structure Factors (923 Kb) Retrieve 2V9D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2V9D from S2C, [Save to disk] Re-refined 2v9d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2V9D 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 2V9D

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 2V9D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2v9d_A] [2v9d_D] [2v9d_B] [2v9d] [2v9d_C] SWISS-PROT database: [P75682] Domain organization of [YAGE_ECOLI] by SWISSPFAM Domain found in 2V9D: [DHDPS ] by SMART

Other resources with information on 2V9D

Community annotation for 2V9D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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