3D8U Transcription Regulator date May 23, 2008
title The Crystal Structure Of A Purr Family Transcriptional Regul Vibrio Parahaemolyticus Rimd 2210633
authors K.Tan, C.Hatzos, S.Moy, A.Joachimiak, Midwest Center For Structu Genomics (Mcsg)
compound source
Molecule: Purr Transcriptional Regulator
Chain: A, B
Engineered: Yes
 Organism_scientific: Vibrio Parahaemolyticus
Organism_taxid: 670
Strain: Rimd 2210633
Gene: Vpa0232
Expression_system: Escherichia Coli
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg8
symmetry Space Group: P 31 2 1
R_factor 0.214 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.264 126.264 83.760 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.88 Å
ligand MSE enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (3d8u.pdb1.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 3D8U
  • CSU: Contacts of Structural Units for 3D8U
  • Likely Quarternary Molecular Structure file(s) for 3D8U
  • Structure Factors (261 Kb)
  • Retrieve 3D8U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D8U from S2C, [Save to disk]
  • Re-refined 3d8u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3D8U 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 3D8U
  • 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 3D8U, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d8u_A] [3d8u] [3d8u_B]
  • SWISS-PROT database: [Q87JL7]
  • Domain organization of [Q87JL7_VIBPA] by SWISSPFAM
    • Other resources with information on 3D8U
  • Community annotation for 3D8U 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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