2OST

The structure of a bacterial homing endonuclease : I-Ssp6803I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.

Zhao, L.Bonocora, R.P.Shub, D.A.Stoddard, B.L.

(2007) EMBO J 26: 2432-2442

  • DOI: 10.1038/sj.emboj.7601672
  • Primary Citation of Related Structures:  
    2OST

  • PubMed Abstract: 
  • The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD-(D/E)-XK endonuclease - a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases ...

    The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD-(D/E)-XK endonuclease - a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to promote recognition of a single long target site, whereas restriction endonuclease tetramers facilitate cooperative binding and cleavage of two short sites. The limited use of the PD-(D/E)-XK nucleases by mobile introns stands in contrast to their frequent use of LAGLIDADG and HNH endonucleases - which in turn, are rarely incorporated into restriction/modification systems.


    Organizational Affiliation

    Graduate Program in Molecular Biophysics, Structure and Design, University of Washington, Seattle, WA, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative endonucleaseC [auth A], D [auth B], E [auth C], F [auth D]151Synechocystis sp. PCC 6803Mutation(s): 4 
Find proteins for Q57253 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q57253 
Go to UniProtKB:  Q57253
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Synthetic DNA 29 MERA [auth Y]29N/A
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
Synthetic DNA 29 MERB [auth Z]29N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A], H [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.281 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.777α = 90
b = 143.777β = 90
c = 319.179γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description