2DGM	Lyase	date	Mar 14, 2006
title	Crystal Structure Of Escherichia Coli Gadb In Complex With I
authors	M.G.Gruetter, G.Capitani, H.Gut
compound		source
Molecule: Glutamate Decarboxylase Beta Chain: A, B, C, D, E, F Synonym: Gad-Beta, Gadb Ec: 4.1.1.15 Engineered: 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 1	R_factor 0.227 R_Free 0.267
crystal cell	length a length b length c angle alpha angle beta angle gamma 91.336 91.804 93.914 76.65 76.94 78.04
method	X-Ray Diffraction	resolution	1.95 Å
ligand	ACY, FMT, IOD, PEG, PLP	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] (464 Kb) [Save to disk] Biological Unit Coordinates (2dgm.pdb1.gz) 458 Kb LPC: Ligand-Protein Contacts for 2DGM CSU: Contacts of Structural Units for 2DGM Likely Quarternary Molecular Structure file(s) for 2DGM Structure Factors (1493 Kb) Retrieve 2DGM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DGM from S2C, [Save to disk] Re-refined 2dgm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DGM 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 2DGM

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 2DGM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dgm_B] [2dgm] [2dgm_E] [2dgm_A] [2dgm_D] [2dgm_C] [2dgm_F] SWISS-PROT database: [P69910] Domain organization of [DCEB_ECOLI] by SWISSPFAM

Other resources with information on 2DGM

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

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Images from IMB Jena Image Library of Biological Macromolecules.

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