3V9U

Crystal structure of RNase T in complex with a preferred ssDNA (AAT) with two Mg in the active site

Structural Biology Knowledgebase: 3V9U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V9U

Classification: HYDROLASE / DNA

Total Structure Weight: 111414.65


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease T A, B, C, D 235 Escherichia coli EC#: 3.1.13 IUBMB
Mutation: E92G
Gene Name(s): rnt b1652 JW1644
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3') E, F, G, H 7 synthetic

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

A, B, C, D COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, E, F, G, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.185
  • Space Group: P 32
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.25 α = 90.00
b = 46.25 β = 90.00
c = 313.65 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-28
  • Released Date: 2012-07-11
  • Deposition author(s): Hsiao, Y.-Y., Yuan, H.S.

Revision History

  • 2013-06-26
    Type: Citation | Details: Citation update