2YNU Hydrolase date Oct 18, 2012
title Apo Gim-1 With 2mol. Crystal Structures Of Pseudomonas Aerug Gim-1: Active Site Plasticity In Metallo-Beta-Lactamases
authors P.S.Borra, O.Samuelsen, J.Spencer, M.S.Lorentzen, H.K.S.Leiros
compound source
Molecule: Gim-1 Protein
Chain: A, B
Synonym: Metallo-Beta-Lactamase Gim-1
Engineered: Yes
 Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 287
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Star Plyss Prare
symmetry Space Group: P 1 21 1
R_factor 0.1852 R_Free 0.2347
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.788 135.385 40.509 90.00 90.23 90.00
method X-Ray Diffractionresolution 2.06 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structures of Pseudomonas aeruginosa GIM-1: active-site plasticity in metallo-beta-lactamases., Borra PS, Samuelsen O, Spencer J, Walsh TR, Lorentzen MS, Leiros HK, Antimicrob Agents Chemother. 2013 Feb;57(2):848-54. doi: 10.1128/AAC.02227-12., Epub 2012 Dec 3. PMID:23208706
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (2ynu.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (2ynu.pdb2.gz) 67 Kb
  • CSU: Contacts of Structural Units for 2YNU
  • Structure Factors (434 Kb)
  • Retrieve 2YNU in mmCIF format [Save to disk]
  • Re-refined 2ynu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YNU 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 2YNU
  • 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 2YNU, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ynu_A] [2ynu_B] [2ynu]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YNU: [Lactamase_B ] by SMART
    • Other resources with information on 2YNU
  • Community annotation for 2YNU at PDBWiki (http://pdbwiki.org)

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