1MOW

E-DreI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Design, Activity and Structure of a Highly Specific Artificial Endonuclease

Chevalier, B.S., Kortemme, T., Chadsey, M.S., Baker, D., Monnat Jr., R.J., Stoddard, B.L.

(2002) Mol Cell 10: 895-905

  • DOI: 10.1016/s1097-2765(02)00690-1
  • Primary Citation of Related Structures:  
    1MOW

  • PubMed Abstract: 

    • We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-DmoI and I-CreI and creating a new 1400 A(2) protein interface between these domains. Protein engineering was accomplished by combining computational redesign and an in vivo protein-folding screen ...

    We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-DmoI and I-CreI and creating a new 1400 A(2) protein interface between these domains. Protein engineering was accomplished by combining computational redesign and an in vivo protein-folding screen. The resulting enzyme, E-DreI (Engineered I-DmoI/I-CreI), binds a long chimeric DNA target site with nanomolar affinity, cleaving it precisely at a rate equivalent to its natural parents. The structure of an E-DreI/DNA complex demonstrates the accuracy of the protein interface redesign algorithm and reveals how catalytic function is maintained during the creation of the new endonuclease. These results indicate that it may be possible to generate novel highly specific DNA binding proteins from homing endonucleases.

    Organizational Affiliation: 

    Fred Hutchinson Cancer Research Center and Graduate Program in Molecular and Cell Biology, University of Washington, 1100 Fairview Avenue N. A3-023, Seattle, WA 98109, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreII [auth A],
J [auth D],
K [auth G],
L [auth J]		260Desulfurococcus mucosus, Chlamydomonas reinhardtii
This entity is chimeric		Mutation(s): 0 
EC: 3.1
UniProt
Find proteins for P21505 (Desulfurococcus mucosus)
Explore P21505 
Go to UniProtKB:  P21505
Find proteins for P05725 (Chlamydomonas reinhardtii)
Explore P05725 
Go to UniProtKB:  P05725
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP05725P21505
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'A [auth B],
C [auth E],
E [auth H],
G [auth K]		23N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'B [auth C],
D [auth F],
F [auth I],
H [auth L]		23N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
JA [auth D],
KA [auth D],
LA [auth D],
MA [auth D],
U [auth A],
JA [auth D],
KA [auth D],
LA [auth D],
MA [auth D],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
M [auth B],
N [auth B],
NA [auth D],
OA [auth D],
P [auth E],
PA [auth D],
Q [auth F],
QA [auth D],
RA [auth D],
SA [auth D],
TA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
HA [auth D],
IA [auth D],
O [auth E],
R [auth A],
S [auth A],
HA [auth D],
IA [auth D],
O [auth E],
R [auth A],
S [auth A],
T [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.76α = 90
b = 131.76β = 90
c = 120.91γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy