4LOX

Crystal structure of the I-SmaMI LAGLIDADG homing endonuclease bound to cleaved DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a LAGLIDADG endonuclease from the Sordaria Macrospore.

Chik, J.Shen, B.Stoddard, B.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LAGLIDADG homing endonuclease I-SmaMI302Sordaria macrospora k-hellMutation(s): 0 
Gene Names: Cytochrome c oxidase subunit 1mitochondrial Introne encodedSMAC_12671
UniProt
Find proteins for F7WD42 (Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell))
Explore F7WD42 
Go to UniProtKB:  F7WD42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7WD42
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3')14N/A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3')11N/A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3')15N/A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')10N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.284α = 90
b = 67.429β = 90
c = 98.09γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description