5TMA Cell Adhesion date Oct 12, 2016
title Zymomonas Mobilis Pyruvate Decarboxylase Mutant Pdc-2.3
authors P.M.Alahuhta, V.V.Lunin
compound source
Molecule: Pyruvate Decarboxylase
Chain: A, B
Synonym: Pdc
Ec: 4.1.1.1
Engineered: Yes
 Organism_scientific: Zymomonas Mobilis
Organism_taxid: 542
Gene: Pdc, Zmo1360
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.170 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.440 124.440 173.825 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.67 Å
ligand EDO, MG, SO4, TPP enzyme Lyase E.C.4.1.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAn iterative computational design approach to increase the thermal endurance of a mesophilic enzyme., Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ, Biotechnol Biofuels. 2018 Jul 9;11:189. doi: 10.1186/s13068-018-1178-9., eCollection 2018. PMID:30002729
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (213 Kb) [Save to disk]
  • Biological Unit Coordinates (5tma.pdb1.gz) 404 Kb
  • LPC: Ligand-Protein Contacts for 5TMA
  • CSU: Contacts of Structural Units for 5TMA
  • Structure Factors (2851 Kb)
  • Retrieve 5TMA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TMA from S2C, [Save to disk]
    • View 5TMA 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 5TMA
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tma_A] [5tma_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5TMA
  • Community annotation for 5TMA at PDBWiki (http://pdbwiki.org)

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