2W27 Signaling Protein date Oct 24, 2008
title Crystal Structure Of The Bacillus Subtilis Ykui Protein, Wit Domain, In Complex With Substrate C-Di-Gmp And Calcium
authors S.Padavattan, W.F.Anderson, T.Schirmer
compound source
Molecule: Ykui Protein
Chain: A, B
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pmcsg7
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.167 124.521 168.751 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 5GP, CA enzyme
Primary referenceCrystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodiester bond cleavage by EAL domains., Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Basle A, Massa C, Collart FR, Schirmer T, Anderson WF, J Biol Chem. 2009 Feb 24. PMID:19244251
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (2w27.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 2W27
  • CSU: Contacts of Structural Units for 2W27
  • Likely Quarternary Molecular Structure file(s) for 2W27
  • Structure Factors (155 Kb)
  • Retrieve 2W27 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W27 from S2C, [Save to disk]
  • Re-refined 2w27 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W27 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 2W27
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2W27, from MSDmotif at EBI
  • Fold representative 2w27 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w27_B] [2w27_A] [2w27]
  • SWISS-PROT database: [O35014]
  • Domain organization of [YKUI_BACSU] by SWISSPFAM
  • Domain found in 2W27: [EAL ] by SMART
  • Other resources with information on 2W27
  • Community annotation for 2W27 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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