5L6L Hydrolase date May 30, 2016
title Structure Of Caulobacter Crescentus Vapbc1 Bound To Operator
authors K.L.Bendtsen, K.Xu, M.Luckmann, D.E.Brodersen
compound source
Molecule: Vapb Family Protein
Chain: A, D, E, H
Engineered: Yes
 Organism_scientific: Caulobacter Crescentus
Organism_taxid: 190650
Strain: Atcc 19089 Cb15
Gene: Cc_0032
Expression_system: Escherichia Coli B
Expression_system_taxid: 37762
Expression_system_variant: B824 (De3)
Expression_system_plasmid: Pkw912hb

Molecule: Ribonuclease Vapc
Chain: B, C, F, G
Synonym: Rnase Vapc,Toxin Vapc
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Caulobacter Crescentus
Organism_taxid: 190650
Strain: Atcc 19089 Cb15
Gene: Vapc, Cc_0031
Expression_system: Escherichia Coli B
Expression_system_taxid: 37762
Expression_system_variant: B824 (De3)
Expression_system_plasmid: Pkw912hb

Molecule: Dna (27-Mer)
Chain: M
Engineered: Yes
Synthetic: Yes
Organism_scientific: Caulobacter Crescentus Cb15
Organism_taxid: 190650

Molecule: Dna (27-Mer)
Chain: N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Caulobacter Crescentus Cb15
Organism_taxid: 190650
symmetry Space Group: C 2 2 21
R_factor 0.178 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.180 144.160 160.540 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand MSE enzyme Hydrolase E.C.3.1 BRENDA
Gene CC ; CC
Gene
Ontology
ChainFunctionProcessComponent
A, E, H, D


F, B, C, G
  • nuclease activity
  • ribonuclease activity
  • toxin activity


    • Primary referenceToxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding., Bendtsen KL, Xu K, Luckmann M, Winther KS, Shah SA, Pedersen CN, Brodersen DE, Nucleic Acids Res. 2016 Dec 19. pii: gkw1266. doi: 10.1093/nar/gkw1266. PMID:27998932
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (321 Kb) [Save to disk]
  • Biological Unit Coordinates (5l6l.pdb1.gz) 307 Kb
  • LPC: Ligand-Protein Contacts for 5L6L
  • CSU: Contacts of Structural Units for 5L6L
  • Structure Factors (317 Kb)
  • Retrieve 5L6L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L6L from S2C, [Save to disk]
  • Re-refined 5l6l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5L6L 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 5L6L
  • 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: [5l6l_A] [5l6l_F] [5l6l_M] [5l6l_E] [5l6l_B] [5l6l_N] [5l6l_G] [5l6l] [5l6l_C] [5l6l_D] [5l6l_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5L6L
  • Community annotation for 5L6L at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science