1YE5 Structural Genomics, Unknown Function date Dec 28, 2004
title Crystal Structure Of Hypothetical Protein Of Unknown Functio Pyrococcus Horikoshii Ot3
authors J.Jeyakanthan, T.H.Tahirov, Riken Structural Genomicsproteomi Initiative (Rsgi)
compound source
Molecule: Hypothetical Protein Ph0500
Chain: A, B
Engineered: Yes
 Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codon Plus (De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-11a
symmetry Space Group: P 1 21 1
R_factor 0.234 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.342 46.381 62.484 90.00 113.33 90.00
method X-Ray Diffractionresolution 2.00 Å
related structures by homologous chain: 1V96
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • ribonuclease activity


    • Primary referenceStructure of PIN-domain protein PH0500 from Pyrococcus horikoshii., Jeyakanthan J, Inagaki E, Kuroishi C, Tahirov TH, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt, 5):463-8. Epub 2005 Apr 26. PMID:16511069
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1ye5.pdb1.gz) 50 Kb
  • CSU: Contacts of Structural Units for 1YE5
  • Likely Quarternary Molecular Structure file(s) for 1YE5
  • Structure Factors (301 Kb)
  • Retrieve 1YE5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YE5 from S2C, [Save to disk]
  • Re-refined 1ye5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YE5 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 1YE5
  • 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 1YE5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ye5] [1ye5_B] [1ye5_A]
  • SWISS-PROT database: [O58236]
  • Domain organization of [O58236_PYRHO] by SWISSPFAM
    • Other resources with information on 1YE5
  • Community annotation for 1YE5 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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