1YT3

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Structural Biology Knowledgebase: 1YT3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YT3

Classification: HYDROLASE TRANSLATION

Total Structure Weight: 43778.81

Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease D A 375 Escherichia coli EC#: 3.1.26.3 IUBMB
Gene Name(s): rnd b1804 JW1793

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.196
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.00 α = 90.00
b = 80.10 β = 90.00
c = 103.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-09
  • Released Date: 2005-08-09
  • Deposition author(s): Zuo, Y., Wang, Y., Malhotra, A.

Revision History

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