5F6C Hydrolase date Dec 05, 2015
title The Structure Of E. Coli Rnase E Catalytically Inactive Muta Rna Bound
authors K.J.Bandyra, B.F.Luisi
compound source
Molecule: Ribonuclease E
Chain: A
Synonym: Rnase E
Ec: 3.1.26.12
Engineered: Yes
Mutation: Yes
 Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rne, Ams, Hmp1, B1084, Jw1071
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ribonuclease E
Chain: B
Synonym: Rnase E
Ec: 3.1.26.12
Engineered: Yes
Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Rne, Ams, Hmp1, B1084, Jw1071
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'-R(Pgpu)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Rna (5'-R(Pgpupg)-3')
Chain: E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.175 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.619 122.562 122.195 90.00 99.77 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand MG, ZN enzyme Hydrolase E.C.3.1.26.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSubstrate Recognition and Autoinhibition in the Central Ribonuclease RNase E., Bandyra KJ, Wandzik JM, Luisi BF, Mol Cell. 2018 Sep 20. pii: S1097-2765(18)30699-3. doi:, 10.1016/j.molcel.2018.08.039. PMID:30270108
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (326 Kb) [Save to disk]
  • Biological Unit Coordinates (5f6c.pdb1.gz) 320 Kb
  • LPC: Ligand-Protein Contacts for 5F6C
  • CSU: Contacts of Structural Units for 5F6C
  • Structure Factors (548 Kb)
  • Retrieve 5F6C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F6C from S2C, [Save to disk]
  • Re-refined 5f6c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5F6C 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 5F6C
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f6c_A] [5f6c_E] [5f6c] [5f6c_B] [5f6c_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5F6C
  • Community annotation for 5F6C at PDBWiki (http://pdbwiki.org)

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