2WOE Hydrolase date Jul 23, 2009
title Crystal Structure Of The D97n Variant Of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum In Complex With Adp-Ribose
authors C.L.Berthold, H.Wang, S.Nordlund, M.Hogbom
compound source
Molecule: Adp-Ribosyl-[Dinitrogen Reductase] Glycohydrolase
Chain: A, B, C
Synonym: Dinitrogenase Reductase-Activating Glycohydrolas, Eadp-Ribosylglycohydrolase;
Ec: 3.2.2.24
Engineered: Yes
Mutation: Yes
Organism_scientific: Rhodospirillum Rubrum
Organism_taxid: 1085
Strain: S1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 Star (De3)
Expression_system_plasmid: Pgex-6p-2
symmetry Space Group: P 21 21 21
R_factor 0.16710 R_Free 0.20731
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.110 84.360 146.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand AR6, GOL, MN, TLA enzyme Hydrolase E.C.3.2.2.24 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceMechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG., Berthold CL, Wang H, Nordlund S, Hogbom M, Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14247-52. Epub 2009 Aug 12. PMID:19706507
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (2woe.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (2woe.pdb2.gz) 52 Kb
  • Biological Unit Coordinates (2woe.pdb3.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 2WOE
  • CSU: Contacts of Structural Units for 2WOE
  • Structure Factors (4269 Kb)
  • Retrieve 2WOE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2WOE from S2C, [Save to disk]
  • Re-refined 2woe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2WOE 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 2WOE
  • 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 2WOE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2woe_A] [2woe_C] [2woe] [2woe_B]
  • SWISS-PROT database: [P14300]
  • Domain organization of [DRAG_RHORU] by SWISSPFAM
  • Other resources with information on 2WOE
  • Community annotation for 2WOE at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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