6QJC | pdb_00006qjc

Dimethyl disulfide inhibited sulfur oxygenase reductase

• PDB DOI: https://doi.org/10.2210/pdb6QJC/pdb

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


• Deposited: 2019-01-24 Released: 2020-02-05 
• Deposition Author(s): Frazao, C., Klezin, A., Poell, U.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels

Frazao, C., Klezin, A.

To be published.

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)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 142.16 kDa 
• Atom Count: 11,015 
• Modeled Residue Count: 1,228 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfur oxygenase/reductase	A, B, C, D	309	Acidianus ambivalens	Mutation(s): 0  Gene Names: sor EC: 1.13.11.55
UniProt
Find proteins for P29082 (Acidianus ambivalens) Explore P29082  Go to UniProtKB:  P29082

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS
TSY	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O2 S3		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.4	α = 90
b = 158.4	β = 90
c = 227.96	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Frazao, C., Klezin, A., Poell, U.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	--
German Research Foundation (DFG)	Germany	Kl885-6/1

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary