9MRD | pdb_00009mrd

Crystal Structure of TREX1 Homolog Plex9.1 bound to ssDNA

• PDB DOI: https://doi.org/10.2210/pdb9MRD/pdb
• NAKB: 9MRD

• Classification: DNA BINDING PROTEIN
• Organism(s): Danio rerio, DNA molecule
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-07 Released: 2025-01-15 
• Deposition Author(s): Rogers, C.M., Langelaan, D.N.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Insights into Innate Immunity Through Evolutionarily Conserved DEDDh Exonucleases

Rogers, C.M., Langelaan, D.N., Dellaire, G.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.19 kDa 
• Atom Count: 1,848 
• Modeled Residue Count: 189 
• Deposited Residue Count: 199 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exodeoxyribonuclease III	A	195	Danio rerio	Mutation(s): 0  Gene Names: plex9.1, si:ch1073-385f13.3 EC: 3.1.11.2
UniProt
Find proteins for E7FAN2 (Danio rerio) Explore E7FAN2  Go to UniProtKB:  E7FAN2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA(5'-*AP*CP*TP*GP*A-3')	B [auth D]	4	DNA molecule

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	E [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84	α = 90
b = 96.66	β = 90
c = 65.56	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Rogers, C.M., Langelaan, D.N.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2024-06440

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release