3V4R Hydrolase Dna date Dec 15, 2011
title Crystal Structure Of A Uvrb Dimer-Dna Complex
authors M.P.J.Webster, R.Jukes, T.Barrett
compound source
Molecule: Uvrabc System Protein B
Chain: A, B
Synonym: Protein Uvrb, Excinuclease Abc Subunit B, Protein
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Bsu35170, Dina, Uvr, Uvrb
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 8c

Molecule: Dna: 5 -Tactgttt-3
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: Synthesised Dna
symmetry Space Group: P 21 21 21
R_factor 0.180 R_Free 0.219
length a length b length c angle alpha angle beta angle gamma
95.940 100.310 163.630 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 Å
ligand ADP enzyme Hydrolase E.C. BRENDA
A, B
  • nuclease activity

  • Primary referenceCrystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes., Webster MP, Jukes R, Zamfir VS, Kay CW, Bagneris C, Barrett T, Nucleic Acids Res. 2012 Sep 1;40(17):8743-8758. Epub 2012 Jun 30. PMID:22753105
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (379 Kb) [Save to disk]
  • Biological Unit Coordinates (3v4r.pdb1.gz) 370 Kb
  • LPC: Ligand-Protein Contacts for 3V4R
  • CSU: Contacts of Structural Units for 3V4R
  • Structure Factors (211 Kb)
  • Retrieve 3V4R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V4R from S2C, [Save to disk]
  • Re-refined 3v4r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V4R 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 3V4R
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3V4R, from MSDmotif at EBI
  • Fold representative 3v4r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v4r_D] [3v4r] [3v4r_A] [3v4r_B] [3v4r_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3V4R: [DEXDc] [HELICc ] by SMART
  • Other resources with information on 3V4R
  • Community annotation for 3V4R at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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