4GRF

Crystal structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 (Target EFI-501010) from Bacteroides vulgatus

• PDB DOI: https://doi.org/10.2210/pdb4GRF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-24 Released: 2012-10-10 
• Deposition Author(s): Patskovsky, Y., Sampathkumar, P., Toro, R., Bhosle, R., Zencheck, W.D., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Imker, H.J., Hammonds, J., Al-Obaidi, N.F., Stead, M., Love, J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structure of thioredoxin domain of thiol-disulfide oxidoreductase BVU-2223 from Bacteroides vulgatus

Patskovsky, Y., Sampathkumar, P., Toro, R., Bhosle, R., Zencheck, W.D., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Evans, B., Chowdhury, S., Hammonds, J., Al-Obaidi, N.F., Stead, M., Love, J., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.95 kDa 
• Atom Count: 1,287 
• Modelled Residue Count: 140 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thiol-disulfide oxidoreductase	A	152	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_2223
UniProt
Find proteins for A6L2G9 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L2G9  Go to UniProtKB:  A6L2G9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	H [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A], C [auth A], D [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.664	α = 90
b = 52.65	β = 90
c = 82.622	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Patskovsky, Y., Sampathkumar, P., Toro, R., Bhosle, R., Zencheck, W.D., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Imker, H.J., Hammonds, J., Al-Obaidi, N.F., Stead, M., Love, J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description