1OUP Hydrolase Dna date Mar 25, 2003
title Crystal Structure Of The Periplasmic Endonuclease Vvn Comple Octamer Double Stranded Dna
authors H.S.Yuan, C.L.Li
compound source
Molecule: 5'-D(Gpcpgpaptpcpgpc)-3'
Chain: C, D, F
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Gpcpgpaptpc)-3'
Chain: E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Pgpc)-3'
Chain: G
Engineered: Yes

Synthetic: Yes

Molecule: Nuclease
Chain: A, B
Fragment: Residues 19-231
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(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptyb2
symmetry Space Group: P 1 21 1
R_factor 0.191 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.740 50.110 89.610 90.00 97.53 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA enzyme Hydrolase E.C.3.1 BRENDA
related structures by homologous chain: 1OUO
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceDNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site., Li CL, Hor LI, Chang ZF, Tsai LC, Yang WZ, Yuan HS, EMBO J 2003 Aug 1;22(15):4014-25. PMID:12881435
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (1oup.pdb1.gz) 44 Kb
  • Biological Unit Coordinates (1oup.pdb2.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 1OUP
  • CSU: Contacts of Structural Units for 1OUP
  • Likely Quarternary Molecular Structure file(s) for 1OUP
  • Structure Factors (240 Kb)
  • Retrieve 1OUP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OUP from S2C, [Save to disk]
  • Re-refined 1oup structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OUP 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 1OUP
  • 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
  • 3D motif for 1OUP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1oupa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1oupb_, region B [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1oup] [1oup_A] [1oup_E] [1oup_B] [1oup_C] [1oup_F] [1oup_D] [1oup_G]
  • SWISS-PROT database: [Q7MHK3]
  • Domain organization of [Q7MHK3_VIBVY] by SWISSPFAM
  • Other resources with information on 1OUP
  • Community annotation for 1OUP 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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