4Z1X | pdb_00004z1x

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

• PDB DOI: https://doi.org/10.2210/pdb4Z1X/pdb
• NAKB: 4Z1X

• Classification: Hydrolase/DNA
• Organism(s): synthetic construct, Fusarium graminearum PH-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-03-27 Released: 2015-04-22 
• Deposition Author(s): Stoddard, B.L., Lambert, A.R., Kulshina, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

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

Stoddard, B.L., Lambert, A.R., 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: 102.64 kDa 
• Atom Count: 6,906 
• Modeled Residue Count: 688 
• Deposited Residue Count: 706 
• 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]	299	Fusarium graminearum PH-1	Mutation(s): 7  Gene Names: nad2
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 (27-MER)	A [auth C], C [auth E]	27	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	B [auth D], D [auth F]	27	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth A], H [auth A], I [auth B], 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:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.833	α = 90
b = 61.186	β = 116.3
c = 128.871	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Stoddard, B.L., Lambert, A.R., Kulshina, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM49857
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	RL1 CA133833

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description