1UCR | pdb_00001ucr

Three-dimensional crystal structure of dissimilatory sulfite reductase D (DsrD)

• PDB DOI: https://doi.org/10.2210/pdb1UCR/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-04-18 Released: 2003-10-14 
• Deposition Author(s): Mizuno, N., Voordouw, G., Miki, K., Sarai, A., Higuchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.180 (Depositor) 
• R-Value Work: 
  0.136 (Depositor) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

Crystal Structure of Dissimilatory Sulfite Reductase D (DsrD) Protein-Possible Interaction with B- and Z-DNA by Its Winged-Helix Motif

Mizuno, N., Voordouw, G., Miki, K., Sarai, A., Higuchi, Y.

(2003) Structure 11: 1133-1140

• PubMed: 12962631 
• DOI: https://doi.org/10.1016/s0969-2126(03)00156-4
• Primary Citation of Related Structures:  
  1UCR


• PubMed Abstract: 
  

  The crystal structure of DsrD from Desulfovibrio vulgaris Hildenborough has been determined at 1.2 A resolution. DsrD is in a dimeric form in the crystal, and five sulfate anions were located on the surface. The structure of DsrD comprises a winged-helix motif, which shows the highest structural homology to similar motifs found in Z-DNA binding proteins and some B-DNA binding proteins. The core structure of the molecule is constructed by intramolecular interactions of hydrophobic residues, which are well conserved in DNA binding proteins, suggesting that these proteins belong to the same superfamily on the basis of the structure. These results indicate a possible role of DsrD in transcription or translation of genes for enzymes catalyzing dissimilatory sulfite reduction.

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Organizational Affiliation: 

Division of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.16 kDa 
• Atom Count: 1,450 
• Modelled Residue Count: 149 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein dsvD	A, B	78	Nitratidesulfovibrio vulgaris	Mutation(s): 0
UniProt
Find proteins for Q46582 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q46582  Go to UniProtKB:  Q46582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.180 (Depositor) 
• R-Value Work:  0.136 (Depositor) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.025	α = 90
b = 64.559	β = 90
c = 45.218	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MOSFLM	data reduction
CCP4	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-14 
Deposition Author(s): Mizuno, N., Voordouw, G., Miki, K., Sarai, A., Higuchi, Y.

Revision History  

• Version 1.0: 2003-10-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations