7P1Y | pdb_00007p1y

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.227 (Depositor), 0.229 (DCC)
R-Value Work:
0.191 (Depositor), 0.193 (DCC)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

A small alarmone hydrolase TdActApo2 mutant - T78N

Jin, Y., Roth, C., Rizkallah, P.

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q73M21
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain H [auth CCC] SDF format, chain F [auth DDD] SDF format, chain E [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain H [auth CCC] MOL2 format, chain F [auth DDD] MOL2 format, chain E [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain H [auth CCC] mmCIF format, chain F [auth DDD] mmCIF format, chain E [auth BBB]	E [auth BBB], F [auth DDD], H [auth CCC], J [auth AAA]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth BBB] Focus chain F [auth DDD] Focus chain H [auth CCC] Focus chain J [auth AAA] Interactions & Density Focus chain E [auth BBB] Focus chain F [auth DDD] Focus chain H [auth CCC] Focus chain J [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain G [auth CCC] MOL2 format, chain I [auth AAA] MOL2 format, chain G [auth CCC] mmCIF format, chain I [auth AAA] mmCIF format, chain G [auth CCC]	G [auth CCC], I [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth CCC] Focus chain I [auth AAA] Interactions & Density Focus chain G [auth CCC] Focus chain I [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.227 (Depositor), 0.229 (DCC)
R-Value Work: 0.191 (Depositor), 0.193 (DCC)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-07-13
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.