7P1Y

A small alarmone hydrolase TdActApo2 mutant - T78N

• PDB DOI: https://doi.org/10.2210/pdb7P1Y/pdb

• Classification: HYDROLASE
• Organism(s): Treponema denticola ATCC 35405
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-07-02 Released: 2022-07-13 
• Deposition Author(s): Jin, Y., Roth, C., Rizkallah, P.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.227 
• R-Value Work: 0.191 

Literature

A small alarmone hydrolase TdActApo2 mutant - T78N

Jin, Y., Roth, C., Rizkallah, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.62 kDa 
• Atom Count: 5,609 
• Modelled Residue Count: 688 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein	A [auth BBB], B [auth DDD], C [auth CCC], D [auth AAA]	232	Treponema denticola ATCC 35405	Mutation(s): 1  Gene Names: TDE_1690
UniProt
Find proteins for Q73M21 (Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104)) Explore Q73M21  Go to UniProtKB:  Q73M21

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	E [auth BBB], F [auth DDD], H [auth CCC], J [auth AAA]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	G [auth CCC], I [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.227 
• R-Value Work: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.286	α = 90
b = 69.189	β = 93.015
c = 132.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Jin, Y., Roth, C., Rizkallah, P.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209057/Z/17/Z

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description