1SIJ | pdb_00001sij

Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-

• PDB DOI: https://doi.org/10.2210/pdb1SIJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Megalodesulfovibrio gigas
• Mutation(s): No 


• Deposited: 2004-03-01 Released: 2004-07-27 
• Deposition Author(s): Boer, D.R., Thapper, A., Brondino, C.D., Romao, M.J., Moura, J.J.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.223 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure and EPR Spectra of "Arsenite-Inhibited" Desulfovibriogigas Aldehyde Dehydrogenase: A Member of the Xanthine Oxidase Family

Boer, D.R., Thapper, A., Brondino, C.D., Romao, M.J., Moura, J.J.G.

(2004) J Am Chem Soc 126: 8614-8615

• PubMed: 15250689 
• DOI: https://doi.org/10.1021/ja0490222
• Primary Citation Related Structures: 
  1SIJ


• PubMed Abstract: 
  

  X-ray crystallography has been used to determine the structure of arsenite-inhibited aldehyde dehydrogenase from Desulfovibrio gigas, a member of the xanthine oxidase family of mononuclear molybdenum enzymes. The structure shows an AsO3 moiety bound to the molybdenum atom of the active site through one of the oxygen atoms. A reduced sample of arsenite-inhibited aldehyde dehydrogenase has a Mo(V) signal that shows anisotropic hyperfine and quadrupole coupling to one arsenic atom. This signal has a strong resemblance with a previously reported signal for arsenite-inhibited xanthine oxidase.

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Organizational Affiliation: 
• REQUIMTE-Departamento de Química, CQFB, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 98.61 kDa 
• Atom Count: 7,363 
• Modeled Residue Count: 907 
• Deposited Residue Count: 907 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde oxidoreductase	A	907	Megalodesulfovibrio gigas	Mutation(s): 0  EC: 1.2.3.1 (PDB Primary Data), 1.2.99.7 (UniProt)
UniProt
Find proteins for Q46509 (Megalodesulfovibrio gigas) Explore Q46509  Go to UniProtKB:  Q46509

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCD	G [auth A]	(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) C19 H26 Mo N8 O16 P2 S2 YEBYDVFRFUQMER-MQPNXHJTSA-L
FES	I [auth A], J [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
AST	H [auth A]	ARSENITE As O3 OWTFKEBRIAXSMO-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.223 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.78	α = 90
b = 142.78	β = 90
c = 161.577	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
Not	model building
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Boer, D.R., Thapper, A., Brondino, C.D., Romao, M.J., Moura, J.J.G.

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description