2BAS Signaling Protein date Oct 14, 2005
title Crystal Structure Of The Bacillus Subtilis Ykui Protein, Wit Domain.
authors G.Minasov, J.S.Brunzelle, L.Shuvalova, D.J.Miller, F.R.Collart, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Gen (Mcsg)
compound source
Molecule: Ykui Protein
Chain: A, B
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Ykui
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21-De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg7
symmetry Space Group: P 21 21 21
R_factor 0.203 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.335 125.271 167.962 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.61 Å
ligand BME, MSE 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] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (2bas.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 2BAS
  • CSU: Contacts of Structural Units for 2BAS
  • Likely Quarternary Molecular Structure file(s) for 2BAS
  • Structure Factors (223 Kb)
  • Retrieve 2BAS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BAS from S2C, [Save to disk]
  • Re-refined 2bas structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BAS 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 2BAS
  • 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 2BAS, from MSDmotif at EBI
  • Fold representative 2bas from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bas] [2bas_A] [2bas_B]
  • SWISS-PROT database: [O35014]
  • Domain organization of [YKUI_BACSU] by SWISSPFAM
  • Domain found in 2BAS: [EAL ] by SMART
  • Other resources with information on 2BAS
  • Community annotation for 2BAS 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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