4EFJ | pdb_00004efj

Crystal structure of I-GzeII LAGLIDADG homing endonuclease in complex with DNA target site

• PDB DOI: https://doi.org/10.2210/pdb4EFJ/pdb
• NAKB: 4EFJ

• Classification: HYDROLASE/DNA
• Organism(s): Fusarium graminearum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-29 Released: 2012-05-02 
• Deposition Author(s): Kulshina, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of I-GzeMII LAGLIDADG homing endonuclease in complex with DNA target site

Kulshina, N.

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)

Macromolecule Content 

• Total Structure Weight: 102.9 kDa 
• Atom Count: 6,846 
• Modeled Residue Count: 688 
• Deposited Residue Count: 708 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LAGLIDADG endonuclease	E [auth A], F [auth B]	300	Fusarium graminearum	Mutation(s): 0  Gene Names: nad2, small subunit ribosomal RNA gene EC: 3.1
UniProt
Find proteins for A5J036 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1)) Explore A5J036  Go to UniProtKB:  A5J036

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA target site top strand	A [auth C], C [auth E]	27	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA target site bottom strand	B [auth D], D [auth F]	27	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth C], H [auth A], I [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.827	α = 90
b = 61.178	β = 116.3
c = 128.877	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: 2012-05-02 
Deposition Author(s): Kulshina, N.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2013-04-03
  Changes: Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description