1O8D Hydrolase date Nov 27, 2002
title Pectate Lyase C From Erwinia Chrysanthemi At Ph 11.2 With 5m
authors S.R.Herron, F.A.Jurnak
compound source
Molecule: Pectate Lyase C
Chain: A
Ec: 4.2.2.2
Engineered: Yes
 Organism_scientific: Erwinia Chrysanthemi
Organism_taxid: 556
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.181 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.670 80.980 95.370 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CA enzyme Lyase E.C.4.2.2.2 BRENDA
related structures by homologous chain: 1O8K, 2PEC
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCharacterization and implications of Ca2+ binding to pectate lyase C., Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F, J Biol Chem 2003 Apr 4;278(14):12271-7. Epub 2003 Jan 22. PMID:12540845
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (1o8d.pdb1.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 1O8D
  • CSU: Contacts of Structural Units for 1O8D
  • Likely Quarternary Molecular Structure file(s) for 1O8D
  • Structure Factors (383 Kb)
  • Retrieve 1O8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O8D from S2C, [Save to disk]
  • Re-refined 1o8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1O8D 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 1O8D
  • 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 1O8D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o8da_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1o8d_A] [1o8d]
  • SWISS-PROT database: [P11073]
  • Domain organization of [PELC_ERWCH] by SWISSPFAM
  • Domain found in 1O8D: [Amb_all ] by SMART
    • Other resources with information on 1O8D
  • Community annotation for 1O8D 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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