4IME Lyase date Jan 02, 2013
title Crystal Structure Of Pasteurella Multocida N-Acetyl-D-Neuram Lyase K164a Mutant
authors A.J.Fisher, N.Huynh
compound source
Molecule: N-Acetylneuraminate Lyase
Chain: A, B, C, D, E, F, G, H
Synonym: N-Acetylneuraminate Pyruvate-Lyase, N-Acetylneuram Aldolase, Sialate Lyase, Sialic Acid Aldolase, Sialic Acid
Ec: 4.1.3.3
Engineered: Yes
Mutation: Yes
Organism_scientific: Pasteurella Multocida Subsp. Gallicida
Organism_taxid: 1169409
Strain: P1059
Gene: Nana, Pm1715
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b(+)
symmetry Space Group: P 1 21 1
R_factor 0.175 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.140 147.710 111.980 90.00 98.51 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand ME2, PG6 enzyme Lyase E.C.4.1.3.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceStructural basis for substrate specificity and mechanism of <i>N</i>-acetyl-D-neuraminic acid lyase from <i>Pasteurella multocida.</i>, Huynh N, Aye A, Li Y, Yu H, Cao H, Tiwari VK, Shin DW, Chen X, Fisher AJ, Biochemistry. 2013 Oct 23. PMID:24152047
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (802 Kb) [Save to disk]
  • Biological Unit Coordinates (4ime.pdb1.gz) 399 Kb
  • Biological Unit Coordinates (4ime.pdb2.gz) 398 Kb
  • LPC: Ligand-Protein Contacts for 4IME
  • CSU: Contacts of Structural Units for 4IME
  • Structure Factors (4110 Kb)
  • Retrieve 4IME in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IME from S2C, [Save to disk]
  • Re-refined 4ime structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IME 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 4IME
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4IME, from MSDmotif at EBI
  • Fold representative 4ime from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ime_G] [4ime_H] [4ime] [4ime_B] [4ime_A] [4ime_D] [4ime_F] [4ime_E] [4ime_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4IME: [DHDPS ] by SMART
  • Other resources with information on 4IME
  • Community annotation for 4IME at PDBWiki (http://pdbwiki.org)

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