7UNO | pdb_00007uno

Thiol-disulfide oxidoreductase TsdA, C129S mutant, from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb7UNO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-04-11 Released: 2022-04-20 
• Deposition Author(s): Osipiuk, J., Reardon-Robinson, M., Nguyen, M.T., Sanchez, B., Ton-That, H., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.134 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

Thiol-disulfide oxidoreductase in Corynebacterium diphtheriae

Osipiuk, J., Reardon-Robinson, M., Nguyen, M.T., Sanchez, B., Ton-That, H., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.07 kDa 
• Atom Count: 2,498 
• Modeled Residue Count: 246 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin domain-containing protein	A	260	Corynebacterium diphtheriae	Mutation(s): 1  Gene Names: CIP107518_01391
UniProt
Find proteins for Q6NJK4 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NJK4  Go to UniProtKB:  Q6NJK4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.134 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37uno

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.809	α = 90
b = 65.114	β = 90
c = 69.422	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-20 
Deposition Author(s): Osipiuk, J., Reardon-Robinson, M., Nguyen, M.T., Sanchez, B., Ton-That, H., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	5R01DE025015-08

Revision History  

• Version 1.0: 2022-04-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description