2YAX

IODOACETAMIDE INHIBITED SULFUR OXYGENASE REDUCTASE

PDB DOI: https://doi.org/10.2210/pdb2YAX/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: 1.80 Å
R-Value Free: 0.193
R-Value Work: 0.169
R-Value Observed: 0.174

wwPDB Validation

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This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 218.98 kDa
Atom Count: 15,532
Modelled Residue Count: 1,842
Deposited Residue Count: 1,908
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFUR OXYGENASE/REDUCTASE	A, D, E	318	Acidianus ambivalens	Mutation(s): 0 EC: 1.13.11.55
UniProt
Find proteins for P29082 (Acidianus ambivalens) Explore P29082 Go to UniProtKB: P29082
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29082
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFUR OXYGENASE/REDUCTASE	B, C, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29082
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, D, E	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS
YCM Query on YCM	B, C, F	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.193
R-Value Work: 0.169
R-Value Observed: 0.174
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.897	α = 90
b = 161.897	β = 90
c = 154.273	γ = 90

Software Package:

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

Structure Validation

Currently 2YAX does not have a validation slider image.

Entry History

Deposition Data

Released Date: 2011-12-21

Deposition Author(s):

Revision History (Full details and data files)

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