6AF4 | pdb_00006af4

Toxin-Antitoxin module from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb6AF4/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: 2.65 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.216 (Depositor), 0.219 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 110.05 kDa
Atom Count: 6,810
Modeled Residue Count: 834
Deposited Residue Count: 952
Unique protein chains: 2

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UQ08
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UQ20
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.254 (Depositor), 0.258 (DCC)
R-Value Work: 0.216 (Depositor), 0.219 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.903	α = 90
b = 73.403	β = 90.08
c = 98.321	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

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: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.