8ZWT | pdb_00008zwt

Crystal structure of atypical two cysteine thiol peroxidase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb8ZWT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-13 Released: 2025-06-18
Deposition Author(s): Shukla, M., Maji, S., Yadav, V.K., Bhattacharyya, S.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.207 (Depositor), 0.215 (DCC)
R-Value Work:
0.170 (Depositor), 0.176 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of atypical two cysteine thiol peroxidase from Staphylococcus aureus

Shukla, M., Maji, S., Yadav, V.K., Bhattacharyya, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.2 kDa
Atom Count: 2,817
Modeled Residue Count: 326
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol peroxidase	A, B	164	Staphylococcus aureus	Mutation(s): 0 Gene Names: tpx, SACOL1762 EC: 1.11.1.24
UniProt
Find proteins for Q5HF61 (Staphylococcus aureus (strain COL)) Explore Q5HF61 Go to UniProtKB: Q5HF61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HF61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTU Query on DTU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.207 (Depositor), 0.215 (DCC)
R-Value Work: 0.170 (Depositor), 0.176 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.061	α = 90
b = 71.911	β = 90
c = 88.324	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Bhattacharyya, S.

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	SRG/2020/001353

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release

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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.