4LYD Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1 date
authors Ghosh, S., Bolin, J.T., Bhowmik, S.
compound source
symmetry
R_factor
R_Free 0.2606
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.26
Gene SWIT
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites., Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD, Biochemistry. 2013 Aug 20;52(33):5685-95. doi: 10.1021/bi400774m. Epub 2013 Aug, 9. PMID:23879719
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (4lyd.pdb1.gz) 84 Kb
  • CSU: Contacts of Structural Units for 4LYD
  • Structure Factors (249 Kb)
  • Retrieve 4LYD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4LYD from S2C, [Save to disk]
  • Re-refined 4lyd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4LYD 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 4LYD
  • 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 4LYD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4lyd] [4lyd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4LYD
  • Community annotation for 4LYD at PDBWiki (http://pdbwiki.org)

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