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)

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
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Literature

Structure of T4 RNA Ligase 1 bound to ATP and Mg

Wimberly-Gard, G.M., Shuman, S.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00971
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain B MOL2 format, chain C [auth B] MOL2 format, chain B mmCIF format, chain C [auth B] mmCIF format, chain B	B, C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B Focus chain C [auth B] Interactions & Density Focus chain B Focus chain C [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Wimberly-Gard, G.M.

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

Revision History (Full details and data files)

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

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