3F9B Hydrolase date Nov 13, 2008
title W354f Yersinia Enterocolitica Ptpase Complexed With Divanada
authors T.A.S.Brandao, H.Robinson, S.J.Johnson, A.C.Hengge
compound source
Molecule: Tyrosine-Protein Phosphatase Yoph
Chain: A
Fragment: Yoph Catalytic Domain: Unp Residues 164-468
Synonym: Virulence Protein
Ec: 3.1.3.48
Engineered: Yes
Mutation: Yes
Organism_scientific: Yersinia Enterocolitica (Type O:9)
Organism_taxid: 34055
Strain: W22703 Serotype O:9 Biotype 2
Gene: Yoph, Yop51
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt7-7
symmetry Space Group: P 21 21 21
R_factor 0.173 R_Free 0.196
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.196 58.191 90.347 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.42 Å
ligand GOL, PDV, VO4 enzyme Hydrolase E.C.3.1.3.48 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceImpaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures., Brandao TA, Robinson H, Johnson SJ, Hengge AC, J Am Chem Soc. 2009 Jan 21;131(2):778-86. PMID:19140798
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (3f9b.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 3F9B
  • CSU: Contacts of Structural Units for 3F9B
  • Likely Quarternary Molecular Structure file(s) for 3F9B
  • Structure Factors (648 Kb)
  • Retrieve 3F9B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F9B from S2C, [Save to disk]
  • Re-refined 3f9b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F9B 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 3F9B
  • 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 3F9B, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f9b] [3f9b_A]
  • SWISS-PROT database: [P15273]
  • Domain organization of [YOPH_YEREN] by SWISSPFAM
  • Domain found in 3F9B: [PTPc ] by SMART
  • Other resources with information on 3F9B
  • Community annotation for 3F9B 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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