1X8D Biosynthetic Protein date Aug 18, 2004
title Crystal Structure Of E. Coli Yiil Protein Containing L-Rhamn
authors K.S.Ryu, J.I.Kim, S.J.Cho, D.Park, C.Park, J.O.Lee, B.S.Choi
compound source
Molecule: Hypothetical Protein Yiil
Chain: A, B, C, D
Synonym: L-Rhamnose Mutarotase
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b
symmetry Space Group: P 1 21 1
R_factor 0.235 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.358 51.311 80.492 90.00 107.82 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand RNS enzyme
note 1X8D is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural Insights into the Monosaccharide Specificity of Escherichia coli Rhamnose Mutarotase., Ryu KS, Kim JI, Cho SJ, Park D, Park C, Cheong HK, Lee JO, Choi BS, J Mol Biol 2005 May 27;349(1):153-62. Epub 2005 Apr 7. PMID:15876375
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (1x8d.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (1x8d.pdb2.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 1X8D
  • CSU: Contacts of Structural Units for 1X8D
  • Likely Quarternary Molecular Structure file(s) for 1X8D
  • Structure Factors (626 Kb)
  • Retrieve 1X8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1X8D from S2C, [Save to disk]
  • Re-refined 1x8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1X8D 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 1X8D
  • 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 1X8D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1x8d_C] [1x8d_D] [1x8d_A] [1x8d_B] [1x8d]
  • SWISS-PROT database: [P32156]
  • Domain organization of [RHAM_ECOLI] by SWISSPFAM
  • Other resources with information on 1X8D
  • Community annotation for 1X8D 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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