9DO4 | pdb_00009do4

Structure of T4 RNA Ligase 1 bound to ATP and Mg

• PDB DOI: https://doi.org/10.2210/pdb9DO4/pdb

• Classification: LIGASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-18 Released: 2024-10-02 
• Deposition Author(s): Wimberly-Gard, G.M., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.296 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structure of T4 RNA Ligase 1 bound to ATP and Mg

Wimberly-Gard, G.M., Shuman, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.65 kDa 
• Atom Count: 2,812 
• Modeled Residue Count: 367 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA ligase 1	A [auth B]	395	Tequatrovirus T4	Mutation(s): 0  Gene Names: 63 EC: 6.5.1.3
UniProt
Find proteins for P00971 (Enterobacteria phage T4) Explore P00971  Go to UniProtKB:  P00971

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	B, C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.296 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.197	α = 90
b = 40.114	β = 116.37
c = 107.032	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: 2024-10-02 
Deposition Author(s): Wimberly-Gard, G.M., Shuman, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM126945

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release