1YT3 Hydrolase,Translation date Feb 09, 2005
title Crystal Structure Of Escherichia Coli Rnase D, An Exoribonuc Involved In Structured Rna Processing
authors Y.Zuo, Y.Wang, A.Malhotra
compound source
Molecule: Ribonuclease D
Chain: A
Synonym: Rnase D
Ec: 3.1.26.3
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rnd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.000 80.100 103.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand SO4, ZN enzyme Hydrolase E.C.3.1.26.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • 3'-5'-exoribonuclease activi...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity
  • ribonuclease D activity


  • Primary referenceCrystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing., Zuo Y, Wang Y, Malhotra A, Structure (Camb) 2005 Jul;13(7):973-84. PMID:16004870
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (1yt3.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 1YT3
  • CSU: Contacts of Structural Units for 1YT3
  • Likely Quarternary Molecular Structure file(s) for 1YT3
  • Structure Factors (804 Kb)
  • Retrieve 1YT3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YT3 from S2C, [Save to disk]
  • Re-refined 1yt3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YT3 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 1YT3
  • 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 1YT3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yt3_A] [1yt3]
  • SWISS-PROT database: [P09155]
  • Domain organization of [RND_ECOLI] by SWISSPFAM
  • Domains found in 1YT3: [35EXOc] [HRDC ] by SMART
  • Other resources with information on 1YT3
  • Community annotation for 1YT3 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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