6T3R

Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report



Literature

Visualizing group II intron dynamics between the first and second steps of splicing

Manigrasso, J.Chillon, I.Genna, V.Somarowthu, S.Pyle, A.M.De Vivo, M.Marcia, M.

To be published.

Macromolecules

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Group IIC Intron RibozymeA390Oceanobacillus iheyensis HTE831
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
Group IIC Intron RibozymeB8Oceanobacillus iheyensis
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SPM
Query on SPM

Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.458α = 90
b = 95.1β = 90
c = 222.402γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-10-11 
  • Released Date: 2020-05-13 
  • Deposition Author(s): Marcia, M., Pyle, A.M.

Funding OrganizationLocationGrant Number
Other governmentFranceANR-10-INSB-05-02
Other governmentFranceANR-10-LABX-49-01
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2020-05-13
    Type: Initial release