5ZO5

active state of the nuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.297 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

NrnC, an RNase D-Like Protein FromAgrobacterium, Is a Novel Octameric Nuclease That Specifically Degrades dsDNA but Leaves dsRNA Intact.

Yuan, Z.Gao, F.Yin, K.Gu, L.

(2018) Front Microbiol 9: 3230-3230


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative 3'-5' exonuclease family protein
A, B
212Agrobacterium fabrum str. J-07Mutation(s): 0 
EC: 3.1.13.-
Find proteins for A0A1S7QSB2 (Agrobacterium fabrum str. J-07)
Go to UniProtKB:  A0A1S7QSB2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.297 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.743α = 90.00
b = 121.743β = 90.00
c = 149.971γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-04-12 
  • Released Date: 2019-04-10 
  • Deposition Author(s): Yuan, Z.L., Gu, L.C.

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release