8UBS

Crystal structure of NrdJ-1 split intein fusion

• PDB DOI: https://doi.org/10.2210/pdb8UBS/pdb

• Classification: SPLICING
• Organism(s): marine metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-24 Released: 2024-10-09 
• Deposition Author(s): Kofoed, C., Ye, X., Jeffrey, P.D., Muir, T.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), European Molecular Biology Organization (EMBO)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.221 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: in silico

Literature

Cell surface sculpting using logic-gated protein actuators

Muir, T.W., Kofoed, C., Ye, X., Jeffrey, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration, mass spectrometry

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration, mass spectrometry

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration, mass spectrometry

Macromolecule Content

• Total Structure Weight: 68.22 kDa 
• Atom Count: 5,213 
• Modelled Residue Count: 600 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrdJ-1	A, B, C, D	151	marine metagenome	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT (Subject of Investigation/LOI)	E [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth C], Q [auth C], R [auth D], S [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.221 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.793	α = 90
b = 84.383	β = 90
c = 174.709	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Kofoed, C., Ye, X., Jeffrey, P.D., Muir, T.W.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R01GM086868-25
European Molecular Biology Organization (EMBO)	European Union	EMBO ALTF 1189-2020

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release