2YAV

ZN INHIBITED SULFUR OXYGENASE REDUCTASE

• PDB DOI: https://doi.org/10.2210/pdb2YAV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acidianus ambivalens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-25 Released: 2011-12-21 
• Deposition Author(s): Veith, A., Urich, T., Seyfarth, K., Protze, J., Frazao, C., Kletzin, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.193 
• R-Value Work: 0.164 
• R-Value Observed: 0.162 

Literature

Substrate Pathways and Mechanisms of Inhibition in the Sulfur Oxygenase Reductase of Acidianus Ambivalens.

Veith, A., Urich, T., Seyfarth, K., Protze, J., Frazao, C., Kletzin, A.

(2011) Front Microbiol 2: 37

• PubMed: 21747782 
• DOI: https://doi.org/10.3389/fmicb.2011.00037
• Primary Citation of Related Structures:  
  2YAV, 2YAW, 2YAX


• PubMed Abstract: 
  

  The sulfur oxygenase reductase (SOR) is the initial enzyme of the sulfur oxidation pathway in the thermoacidophilic Archaeon Acidianus ambivalens. The SOR catalyzes an oxygen-dependent sulfur disproportionation to H(2)S, sulfite and thiosulfate. The spherical, hollow, cytoplasmic enzyme is composed of 24 identical subunits with an active site pocket each comprising a mononuclear non-heme iron site and a cysteine persulfide. Substrate access and product exit occur via apolar chimney-like protrusions at the fourfold symmetry axes, via narrow polar pores at the threefold symmetry axes and via narrow apolar pores within in each subunit. In order to investigate the function of the pores we performed site-directed mutagenesis and inhibitor studies.

---

Organizational Affiliation: 

Institute of Microbiology and Genetics, Technische Universität Darmstadt Darmstadt, Germany.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 219.77 kDa 
• Atom Count: 16,413 
• Modelled Residue Count: 1,842 
• Deposited Residue Count: 1,908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFUR OXYGENASE/REDUCTASE	A, B, C, D, E, F	318	Acidianus ambivalens	Mutation(s): 0  EC: 1.13.11.55
UniProt
Find proteins for P29082 (Acidianus ambivalens) Explore P29082  Go to UniProtKB:  P29082

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	BA [auth F], H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	CA [auth F], I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	AA [auth F], G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	DA [auth F], J [auth A], N [auth B], R [auth C], V [auth D], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B, C, D, E, F	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.193 
• R-Value Work: 0.164 
• R-Value Observed: 0.162 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.074	α = 90
b = 162.074	β = 90
c = 154.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Veith, A., Urich, T., Seyfarth, K., Protze, J., Frazao, C., Kletzin, A.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description