1OUP

Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA

Structural Biology Knowledgebase: 1OUP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 1OUP

Classification: HYDROLASE / DNA

Total Structure Weight: 59249.49


Macromolecule Entities
Molecule Chains Length Organism Details
Nuclease A, B 213 Vibrio vulnificus EC#: 3.1 IUBMB
Fragment: residues 19-231
Mutation: H80A, Q163P, T164D, E165R, L166A
Gene Name(s): VV2866
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' C, D, F 8 synthetic
5'-D(*GP*CP*GP*AP*TP*C)-3' E 6 synthetic
5'-D(P*GP*C)-3' G 2 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.191
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 53.74 α = 90.00
b = 50.11 β = 97.53
c = 89.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-25
  • Released Date: 2003-08-05
  • Deposition author(s): Yuan, H.S., Li, C.-L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4