4LOX | pdb_00004lox

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

• PDB DOI: https://doi.org/10.2210/pdb4LOX/pdb
• NAKB: 4LOX

• Classification: HYDROLASE/DNA
• Organism(s): Sordaria macrospora k-hell
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-14 Released: 2014-09-24 
• Deposition Author(s): Chik, J., Shen, B., Stoddard, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a LAGLIDADG endonuclease from the Sordaria Macrospore.

Chik, J., Shen, B., Stoddard, B.

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)

Macromolecule Content 

• Total Structure Weight: 49.44 kDa 
• Atom Count: 3,539 
• Modeled Residue Count: 350 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAGLIDADG homing endonuclease I-SmaMI	A	302	Sordaria macrospora k-hell	Mutation(s): 0  Gene Names: Cytochrome c oxidase subunit 1, mitochondrial Introne encoded, SMAC_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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3')	B	14	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3')	C	11	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3')	D	15	N/A

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')	E	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.284	α = 90
b = 67.429	β = 90
c = 98.09	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Chik, J., Shen, B., Stoddard, B.

Revision History  

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