2RDE	Structural Genomics, Unknown Function	date	Sep 22, 2007
title	Crystal Structure Of Vca0042 Complexed With C-Di-Gmp
authors	J.Benach, S.S.Swaminathan, R.Tamayo, J.Seetharaman, S.Handelman, F.Forouhar, H.Neely, A.Camilli, J.F.Hunt, Northeast Structural Consortium (Nesg)
compound		source
Molecule: Uncharacterized Protein Vca0042 Chain: A, B Engineered: Yes		Organism_scientific: Vibrio Cholerae Organism_taxid: 345073 Strain: O395 Gene: Vca0042, Vc0395_0091 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28b
symmetry	Space Group: P 1	R_factor 0.195 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 47.006 55.400 58.044 99.88 97.09 106.80
method	X-Ray Diffraction	resolution	1.92 Å
ligand	C2E	enzyme
note	2RDE is a representative structure
Gene	VC0395
Gene Ontology	Chain Function Process Component A, B
Primary reference	The structural basis of cyclic diguanylate signal transduction by PilZ domains., Benach J, Swaminathan SS, Tamayo R, Handelman SK, Folta-Stogniew E, Ramos JE, Forouhar F, Neely H, Seetharaman J, Camilli A, Hunt JF, EMBO J. 2007 Dec 12;26(24):5153-66. Epub 2007 Nov 22. PMID:18034161

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk] Biological Unit Coordinates (2rde.pdb1.gz) 84 Kb LPC: Ligand-Protein Contacts for 2RDE CSU: Contacts of Structural Units for 2RDE Likely Quarternary Molecular Structure file(s) for 2RDE Structure Factors (536 Kb) Retrieve 2RDE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2RDE from S2C, [Save to disk] Re-refined 2rde structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2RDE 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 2RDE

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 2RDE, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2rde] [2rde_B] [2rde_A] SWISS-PROT database: [A5F1K1] Domain organization of [A5F1K1_VIBC3] by SWISSPFAM

Other resources with information on 2RDE

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

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---