6AF3 | pdb_00006af3

Toxin-Antitoxin module from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb6AF3/pdb

Classification: TOXIN
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-08-08 Released: 2019-08-14
Deposition Author(s): Kang, S.M., Kim, D.H., Jin, C.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.333 (Depositor), 0.350 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Toxin-Antitoxin module from Streptococcus pneumoniae

Kang, S.M., Kim, D.H., Jin, C.

To be published.

Macromolecule Content

Total Structure Weight: 111.93 kDa
Atom Count: 6,717
Modeled Residue Count: 819
Deposited Residue Count: 952
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HigB toxin	A, C, E, G	141	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: higB
UniProt
Find proteins for A0A0H2UQ08 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQ08 Go to UniProtKB: A0A0H2UQ08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UQ08
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HigA antitoxin	B, D, F, H	97	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: higA
UniProt
Find proteins for A0A0H2UQ20 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQ20 Go to UniProtKB: A0A0H2UQ20
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UQ20
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.333 (Depositor), 0.350 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.575	α = 90
b = 67.038	β = 94.22
c = 87.717	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2018R1A2A1A19018526

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

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.