4E8T

Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)

Structural Biology Knowledgebase: 4E8T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4E8T

Classification: RNA

Total Structure Weight: 133505.19

Macromolecule Entities
Molecule Chains Length Organism Details
Group IIC intron A 393 Oceanobacillus iheyensis
5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3' B 8 synthetic synthetic oligonucleotide

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EPE
Query on EPE

A 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SPM
Query on SPM

A SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.189
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.46 α = 90.00
b = 95.76 β = 90.00
c = 225.69 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2012-03-20
  • Released Date: 2012-11-14
  • Deposition author(s): Marcia, M., Pyle, A.M.

Revision History

No revisions since initial release