5A0W

THE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET DNA AND IN THE PRESENCE OF 2MM MN

• PDB DOI: https://doi.org/10.2210/pdb5A0W/pdb
• NAKB: 5A0W

• Classification: HYDROLASE/DNA
• Organism(s): Desulfurococcus mucosus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-23 Released: 2016-05-11 
• Deposition Author(s): Molina, R., Besker, N., Prieto, J., Montoya, G., D'Abramo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.208 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Structural and Dynamical Characterization of the I- Dmo Catalytic Activity

Molina, R., Besker, N., Prieto, J., Montoya, G., D'Abramo, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.58 kDa 
• Atom Count: 8,087 
• Modelled Residue Count: 701 
• Deposited Residue Count: 747 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HOMING ENDONUCLEASE I-DMOI	A, D, G	199	Desulfurococcus mucosus	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P21505 (Desulfurococcus mucosus) Explore P21505  Go to UniProtKB:  P21505

Entity ID: 2
Molecule	Chains	Length	Organism	Image
25MER	B, E, H	25	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
25MER	C, F, I	25	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	AA [auth I], K [auth A], O [auth C], P [auth C], T [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	L [auth A], N [auth B], R [auth D], U [auth F], V [auth G], Z [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	J [auth A], M [auth A], Q [auth D], S [auth F], W [auth G], X [auth G], Y [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.208 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.928	α = 90
b = 69.77	β = 120.06
c = 106.985	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Molina, R., Besker, N., Prieto, J., Montoya, G., D'Abramo, M.

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description