3BEE Structural Genomics, Unknown Function date Nov 16, 2007
title Crystal Structure Of Putative Yfre Protein From Vibrio Parahaemolyticus
authors C.Chang, C.Hatzos, J.Abdullah, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg)
compound source
Molecule: Putative Yfre Protein
Chain: A, B
Fragment: Residues 146-235
Engineered: Yes
 Organism_scientific: Vibrio Parahaemolyticus Rimd 2210633
Organism_taxid: 223926
Strain: Rimd 2210633 Serotype O3:K6
Gene: Vp1931
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Derivative
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg7
symmetry Space Group: P 43 21 2
R_factor 0.191 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.383 82.383 74.342 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand EDO, MSE enzyme
note 3BEE is a representative structure
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (3bee.pdb1.gz) 17 Kb
  • Biological Unit Coordinates (3bee.pdb2.gz) 16 Kb
  • LPC: Ligand-Protein Contacts for 3BEE
  • CSU: Contacts of Structural Units for 3BEE
  • Likely Quarternary Molecular Structure file(s) for 3BEE
  • Structure Factors (261 Kb)
  • Retrieve 3BEE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BEE from S2C, [Save to disk]
  • Re-refined 3bee structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3BEE 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 3BEE
  • 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 3BEE, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bee_B] [3bee] [3bee_A]
  • SWISS-PROT database: [Q87ND7]
  • Domain organization of [Q87ND7_VIBPA] by SWISSPFAM
    • Other resources with information on 3BEE
  • Community annotation for 3BEE 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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