8U12 | pdb_00008u12

Crystal Structure of Antitoxin Protein Rv0298 of Type II Toxin-antitoxin Systems from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb8U12/pdb

Classification: ANTITOXIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-30 Released: 2023-09-27
Deposition Author(s): Kim, Y., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.186 (Depositor), 0.186 (DCC)
R-Value Work:
0.166 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Antitoxin Protein Rv0298 of Type II Toxin-antitoxin Systems from Mycobacterium tuberculosis

Kim, Y., Tesar, C., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.26 kDa
Atom Count: 3,630
Modeled Residue Count: 396
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin Rv0298	A, B, C, D, E A, B, C, D, E, F, G, H	75	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv0298
UniProt
Find proteins for P9WJ09 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJ09 Go to UniProtKB: P9WJ09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJ09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain K [auth G] SDF format, chain J [auth F] SDF format, chain I [auth D] MOL2 format, chain L [auth H] MOL2 format, chain K [auth G] MOL2 format, chain J [auth F] MOL2 format, chain I [auth D] mmCIF format, chain L [auth H] mmCIF format, chain K [auth G] mmCIF format, chain J [auth F] mmCIF format, chain I [auth D]	I [auth D], J [auth F], K [auth G], L [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth D] Focus chain J [auth F] Focus chain K [auth G] Focus chain L [auth H] Interactions & Density Focus chain I [auth D] Focus chain J [auth F] Focus chain K [auth G] Focus chain L [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.186 (Depositor), 0.186 (DCC)
R-Value Work: 0.166 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.237	α = 90
b = 141.237	β = 90
c = 86.677	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-09-27
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection
Version 1.2: 2024-11-20
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.