2YYU Lyase date May 02, 2007
title Crystal Structure Of Uncharacterized Conserved Protein From Geobacillus Kaustophilus
authors M.Kanagawa, S.Baba, Y.Nakamura, Y.Bessho, S.Kuramitsu, S.Yokoyama G.Sampei, Riken Structural Genomicsproteomics Initiative (R
compound source
Molecule: Orotidine 5'-Phosphate Decarboxylase
Chain: A, B
Synonym: Omp Decarboxylase, Ompdcase, Ompdecase
Ec: 4.1.1.23
Engineered: Yes
Organism_scientific: Geobacillus Kaustophilus
Organism_taxid: 235909
Strain: Hta426
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril-X
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Histev
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.650 70.151 62.865 90.00 106.86 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand C5P enzyme Lyase E.C.4.1.1.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (2yyu.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2YYU
  • CSU: Contacts of Structural Units for 2YYU
  • Likely Quarternary Molecular Structure file(s) for 2YYU
  • Structure Factors (1021 Kb)
  • Retrieve 2YYU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YYU from S2C, [Save to disk]
  • Re-refined 2yyu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YYU 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 2YYU
  • 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 2YYU, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yyu] [2yyu_A] [2yyu_B]
  • SWISS-PROT database: [Q5L0U0]
  • Domain organization of [PYRF_GEOKA] by SWISSPFAM
  • Domain found in 2YYU: [OMPdecase ] by SMART
  • Other resources with information on 2YYU
  • Community annotation for 2YYU 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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