2IVK Hydrolase date Jun 14, 2006
title Crystal Structure Of The Periplasmic Endonuclease Vvn Comple 16-Bp Dna
authors Y.T.Wang, W.J.Yang, C.L.Li, L.G.Doudeva, H.S.Yuan
compound source
Molecule: Endonuclease I
Chain: A, B, C, D
Synonym: Vvn Nuclease
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Vibrio Vulnificus
Organism_taxid: 672
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_variant: De3
Expression_system_vector: Ptyb2

Molecule: 5'-D(Gpapaptptpcpgpaptpcp Gpapaptp
Chain: E, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Apaptptpcpgpaptpcpgp Apaptptp
Chain: F, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Gpapaptptpcpgpaptpcp Gpapaptp
Chain: I, J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.237 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
64.636 64.705 79.157 74.45 73.56 75.56
method X-Ray Diffractionresolution 2.90 Å
enzyme Hydrolase E.C.3.1 BRENDA
A, D, C, B
  • nuclease activity
  • endonuclease activity

  • Primary referenceStructural basis for sequence-dependent DNA cleavage by nonspecific endonucleases., Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS, Nucleic Acids Res. 2007;35(2):584-94. Epub 2006 Dec 15. PMID:17175542
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (184 Kb) [Save to disk]
  • Biological Unit Coordinates (2ivk.pdb1.gz) 179 Kb
  • CSU: Contacts of Structural Units for 2IVK
  • Likely Quarternary Molecular Structure file(s) for 2IVK
  • Structure Factors (358 Kb)
  • Retrieve 2IVK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IVK from S2C, [Save to disk]
  • Re-refined 2ivk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IVK 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 2IVK
  • 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 2IVK, from MSDmotif at EBI
  • Fold representative 2ivk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ivk_A] [2ivk_J] [2ivk_B] [2ivk_H] [2ivk] [2ivk_E] [2ivk_F] [2ivk_I] [2ivk_G] [2ivk_D] [2ivk_C]
  • SWISS-PROT database: [Q7MHK3]
  • Domain organization of [Q7MHK3_VIBVY] by SWISSPFAM
  • Other resources with information on 2IVK
  • Community annotation for 2IVK 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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