2DGK	Lyase	date	Mar 14, 2006
title	Crystal Structure Of An N-Terminal Deletion Mutant Of Escher Gadb In An Autoinhibited State (Aldamine)
authors	M.G.Gruetter, G.Capitani, H.Gut
compound		source
Molecule: Glutamate Decarboxylase Beta Chain: A, B, C, D, E, F Fragment: Gadbd1-14 Synonym: Gad-Beta, Gadb Ec: 4.1.1.15 Engineered: Yes Mutation: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Strain: Jm109 Gene: Gadb Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Jm109 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pqe60
symmetry	Space Group: P 21 21 21	R_factor 0.218 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 92.770 158.560 201.420 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	EDO, PLP, SO4	enzyme	Lyase E.C.4.1.1.15 BRENDA
Gene Ontology	Chain Function Process Component F, A, D, C, E, B
Primary reference	Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB., Gut H, Pennacchietti E, John RA, Bossa F, Capitani G, De Biase D, Grutter MG, EMBO J. 2006 Jun 7;25(11):2643-51. Epub 2006 May 4. PMID:16675957

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (449 Kb) [Save to disk] Biological Unit Coordinates (2dgk.pdb1.gz) 442 Kb Biological Unit Coordinates (2dgk.pdb2.gz) 153 Kb Biological Unit Coordinates (2dgk.pdb3.gz) 152 Kb Biological Unit Coordinates (2dgk.pdb4.gz) 149 Kb Biological Unit Coordinates (2dgk.pdb5.gz) 150 Kb Biological Unit Coordinates (2dgk.pdb6.gz) 151 Kb LPC: Ligand-Protein Contacts for 2DGK CSU: Contacts of Structural Units for 2DGK Likely Quarternary Molecular Structure file(s) for 2DGK Structure Factors (1759 Kb) Retrieve 2DGK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DGK from S2C, [Save to disk] Re-refined 2dgk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DGK 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 2DGK

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 2DGK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dgk_E] [2dgk_A] [2dgk] [2dgk_F] [2dgk_D] [2dgk_C] [2dgk_B] SWISS-PROT database: [P69910] Domain organization of [DCEB_ECOLI] by SWISSPFAM

Other resources with information on 2DGK

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

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