4J7M

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion

Structural Biology Knowledgebase: 4J7M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4J7M

Classification: HYDROLASE / RNA

Total Structure Weight: 45499.31


Macromolecule Entities
Molecule Chains Length Organism Details
Protein Dom3Z A 378 Mus musculus EC#: 3.1.13 IUBMB 3.6.1 IUBMB
Gene Name(s): Dxo Dom3z Ng6
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3') B 5 Synthetic construct 5'-end monophosphorylated oligo RNA with Phosphorothioate link between 1-2 U and 2-3 U

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
UBD
Query on UBD

A URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)
C9 H14 N2 O12 P2
ZPVPRWPOZBXDKD-XVFCMESISA-N
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
U37
Query on U37
B RNA LINKING C9 H13 N2 O8 P S U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.183
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.99 α = 90.00
b = 87.84 β = 111.69
c = 54.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-13
  • Released Date: 2013-03-27
  • Deposition author(s): Chang, J.H., Tong, L.

Revision History

  • 2014-03-12
    Type: Citation | Details: Citation update