3GND	Lyase	date	Mar 17, 2009
title	Crystal Structure Of E. Coli Lsrf In Complex With Ribulose-5
authors	S.T.Miller, Z.C.Diaz
compound		source
Molecule: Aldolase Lsrf Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Fragment: Uncharacterized Aldolase Lsrf Ec: 4.1.2.- Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Strain: K-12 Gene: B1517, Jw1510, Lsrf, Yneb Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: K-12 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-4t1
symmetry	Space Group: P 1	R_factor 0.195 R_Free 0.228
crystal cell	length a length b length c angle alpha angle beta angle gamma 78.741 107.102 169.516 90.00 102.62 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	5RP	enzyme	Lyase E.C.4.1.2 BRENDA
Gene Ontology	Chain Function Process Component S, F, T, N, K, E, Q, M, C, L, A, J, O, P, B, H, D, R, I, G
Primary reference	The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF., Diaz Z, Xavier KB, Miller ST, PLoS One. 2009 Aug 28;4(8):e6820. PMID:19714241

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (853 Kb) [Save to disk] Biological Unit Coordinates (3gnd.pdb1.gz) 425 Kb Biological Unit Coordinates (3gnd.pdb2.gz) 426 Kb LPC: Ligand-Protein Contacts for 3GND CSU: Contacts of Structural Units for 3GND Structure Factors (1584 Kb) Retrieve 3GND in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GND from S2C, [Save to disk] Re-refined 3gnd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GND 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 3GND

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3GND, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gnd_E] [3gnd_N] [3gnd_L] [3gnd_K] [3gnd_B] [3gnd_D] [3gnd] [3gnd_J] [3gnd_O] [3gnd_R] [3gnd_M] [3gnd_F] [3gnd_A] [3gnd_Q] [3gnd_S] [3gnd_T] [3gnd_I] [3gnd_C] [3gnd_H] [3gnd_G] [3gnd_P] SWISS-PROT database: [P76143] Domain organization of [LSRF_ECOLI] by SWISSPFAM Domain found in 3GND: [DeoC ] by SMART

Other resources with information on 3GND

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

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