3BK1 Hydrolase date Dec 05, 2007
title Crystal Structure Analysis Of Rnase J
authors I.L.De La Sierra-Gallay, L.Zig, H.Putzer
compound source
Molecule: Metal Dependent Hydrolase
Chain: A
Fragment: Unp Residues 20-573
Synonym: Rnase J
Ec: 3.-.-.-
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27
Gene: Ttc0775
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: F 2 2 2
R_factor 0.197 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.830 117.620 230.490 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.33 Å
ligand GOL, MSE, SO4, ZN enzyme Hydrolase E.C.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • endoribonuclease activity
  • 5'-3' exoribonuclease activi...


    • Primary referenceStructural insights into the dual activity of RNase J., de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H, Nat Struct Mol Biol. 2008 Feb;15(2):206-12. Epub 2008 Jan 20. PMID:18204464
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (3bk1.pdb1.gz) 182 Kb
  • LPC: Ligand-Protein Contacts for 3BK1
  • CSU: Contacts of Structural Units for 3BK1
  • Likely Quarternary Molecular Structure file(s) for 3BK1
  • Structure Factors (252 Kb)
  • Retrieve 3BK1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BK1 from S2C, [Save to disk]
  • Re-refined 3bk1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3BK1 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 3BK1
  • 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 3BK1, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bk1] [3bk1_A]
  • SWISS-PROT database: [Q72JJ7]
  • Domain organization of [Q72JJ7_THET2] by SWISSPFAM
  • Domain found in 3BK1: [Lactamase_B ] by SMART
    • Other resources with information on 3BK1
  • Community annotation for 3BK1 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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