3IWA

Crystal structure of a FAD-dependent pyridine nucleotide-disulphide oxidoreductase from Desulfovibrio vulgaris

• PDB DOI: https://doi.org/10.2210/pdb3IWA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris DP4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-02 Released: 2009-10-06 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Iizuka, M., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.243 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Crystal structure of a FAD-dependent pyridine nucleotide-disulphide oxidoreductase from Desulfovibrio vulgaris

Bonanno, J.B., Freeman, J., Bain, K.T., Iizuka, M., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 50.59 kDa 
• Atom Count: 2,974 
• Modelled Residue Count: 397 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-dependent pyridine nucleotide-disulphide oxidoreductase	A	472	Nitratidesulfovibrio vulgaris DP4	Mutation(s): 0  Gene Names: Dvul_0176 EC: 1.6
UniProt
Find proteins for A0A0H3A4H3 (Nitratidesulfovibrio vulgaris (strain DP4)) Explore A0A0H3A4H3  Go to UniProtKB:  A0A0H3A4H3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.243 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.564	α = 90
b = 127.564	β = 90
c = 157.713	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Iizuka, M., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references