4B20 Hydrolase date Jul 12, 2012
title Structural Basis Of Dna Loop Recognition By Endonuclease V
authors I.Rosnes, A.D.Rowe, R.J.Forstrom, I.Alseth, M.Bjoras, B.Dalhus
compound source
Molecule: Endonuclease V
Chain: A, B
Synonym: Deoxyinosine 3'Endonuclease, Deoxyribonuclease V,
Ec: 3.1.21.7
Engineered: Yes
Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: 5'-D(Gpcpgpapcpapgp)-3'
Chain: C, F

Synthetic: Yes

Molecule: 5'-D(Aptpcptptpgptpcpgpcp)-3'
Chain: D, G

Synthetic: Yes
symmetry Space Group: I 2 2 2
R_factor 0.2274 R_Free 0.2906
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.231 135.370 194.993 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand MG enzyme Hydrolase E.C.3.1.21.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity, p...


  • Primary referenceStructural basis of DNA loop recognition by endonuclease V., Rosnes I, Rowe AD, Vik ES, Forstrom RJ, Alseth I, Bjoras M, Dalhus B, Structure. 2013 Feb 5;21(2):257-65. doi: 10.1016/j.str.2012.12.007. Epub 2013 Jan, 11. PMID:23313664
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (4b20.pdb1.gz) 44 Kb
  • Biological Unit Coordinates (4b20.pdb2.gz) 45 Kb
  • Biological Unit Coordinates (4b20.pdb3.gz) 86 Kb
  • Biological Unit Coordinates (4b20.pdb4.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 4B20
  • CSU: Contacts of Structural Units for 4B20
  • Structure Factors (244 Kb)
  • Retrieve 4B20 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B20 from S2C, [Save to disk]
  • Re-refined 4b20 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B20 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 4B20
  • 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 4B20, from MSDmotif at EBI
  • Fold representative 4b20 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b20_D] [4b20_C] [4b20_F] [4b20_A] [4b20] [4b20_B] [4b20_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4B20
  • Community annotation for 4B20 at PDBWiki (http://pdbwiki.org)

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