3VA0

Crystal structure of RNase T in complex with a di-nucleotide product (GG) with one Mg in the active site

Structural Biology Knowledgebase: 3VA0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VA0

Classification: HYDROLASE / DNA

Total Structure Weight: 52772.88


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease T A, B 235 Escherichia coli EC#: 3.1.13 IUBMB
Gene Name(s): rnt b1652 JW1644
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*G)-3') C, D 2 synthetic

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.206
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.69 α = 90.00
b = 105.81 β = 90.00
c = 47.07 γ = 90.00

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