5D5F Hydrolase date Aug 10, 2015
title In Meso In Situ Serial X-Ray Crystallography Structure Of Ly Bromine-Sad At 100 K
authors C.Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey
compound source
Molecule: Lysozyme C
Chain: A
Synonym: 1,4-Beta-N-Acetylmuramidase C,Allergen Gal D Iv
Ec: 3.2.1.17
 Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
symmetry Space Group: P 43 21 2
R_factor 0.182 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.390 78.390 37.880 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand ACY, BR, NA, PE5 enzyme Hydrolase E.C.3.2.1.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIn meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures., Huang CY, Olieric V, Ma P, Howe N, Vogeley L, Liu X, Warshamanage R, Weinert T, Panepucci E, Kobilka B, Diederichs K, Wang M, Caffrey M, Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):93-112. doi:, 10.1107/S2059798315021683. Epub 2016 Jan 1. PMID:26894538
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (5d5f.pdb1.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 5D5F
  • CSU: Contacts of Structural Units for 5D5F
  • Structure Factors (318 Kb)
  • Retrieve 5D5F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D5F from S2C, [Save to disk]
  • Re-refined 5d5f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D5F 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 5D5F
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d5f_A] [5d5f]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D5F: [LYZ1 ] by SMART
    • Other resources with information on 5D5F
  • Community annotation for 5D5F at PDBWiki (http://pdbwiki.org)

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