5O6I

Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.

Alba, J.Marcaida, M.J.Prieto, J.Montoya, G.Molina, R.D'Abramo, M.

(2017) J Comput Aided Mol Des 31: 1063-1072

  • DOI: https://doi.org/10.1007/s10822-017-0087-5
  • Primary Citation of Related Structures:  
    5O6G, 5O6I

  • PubMed Abstract: 

    I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.


  • Organizational Affiliation

    Department of Chemistry, Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homing endonuclease I-DmoIA,
D [auth F],
G [auth K]
200Desulfurococcus mucosusMutation(s): 0 
EC: 3.1
UniProt
Find proteins for P21505 (Desulfurococcus mucosus)
Explore P21505 
Go to UniProtKB:  P21505
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21505
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (25-MER)B [auth C],
E [auth G],
H [auth L]
25synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (25-MER)C [auth D],
F [auth I],
I [auth N]
25synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth F]
N [auth F]
P [auth K]
J [auth A],
K [auth A],
M [auth F],
N [auth F],
P [auth K],
Q [auth K]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A],
O [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107α = 90
b = 70.48β = 119.81
c = 107.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description