1WQ2 | pdb_00001wq2

Neutron Crystal Structure Of Dissimilatory Sulfite Reductase D (DsrD)

• PDB DOI: https://doi.org/10.2210/pdb1WQ2/pdb

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


• Deposited: 2004-09-19 Released: 2005-09-19 
• Deposition Author(s): Chatake, T., Mizuno, N., Voordouw, G., Higuchi, Y., Arai, S., Tanaka, I., Niimura, N.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.289 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystallization and preliminary neutron analysis of the dissimilatory sulfite reductase D (DsrD) protein from the sulfate-reducing bacterium Desulfovibrio vulgaris.

Chatake, T., Mizuno, N., Voordouw, G., Higuchi, Y., Arai, S., Tanaka, I., Niimura, N.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2306-2309

• PubMed: 14646103 
• DOI: https://doi.org/10.1107/s0907444903020596
• Primary Citation of Related Structures:  
  1WQ2


• PubMed Abstract: 
  

  Dissimilatory sulfite reductase D (DsrD) from Desulfovibrio vulgaris has been crystallized for a neutron diffraction study. The initial crystals obtained were too small for the neutron experiment. In order to obtain a larger crystal (>1 mm3), a combination of two techniques was developed to determine the optimum crystallization conditions: a crystallization phase diagram was obtained, followed by crystal-quality assessment via X-ray diffraction. Using conditions determined in this manner, a large single crystal (1.7 mm3) of DsrD protein was subsequently grown in D(2)O solution by the macroseeding technique. A neutron diffraction experiment was carried out using the BIX-3 diffractometer at the Japan Atomic Energy Research Institute (JAERI), collecting data to 2.4 A resolution from an optimized crystal.

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Organizational Affiliation: 

Neutron Structural Biology, Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195, 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: 17.78 kDa 
• Atom Count: 1,080 
• Modelled Residue Count: 131 
• 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 B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.289 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.5	α = 90
b = 65.1	β = 90
c = 46.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-19 
Deposition Author(s): Chatake, T., Mizuno, N., Voordouw, G., Higuchi, Y., Arai, S., Tanaka, I., Niimura, N.

Revision History  

• Version 1.0: 2005-09-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2018-03-07
  Changes: Advisory, Atomic model, Data collection
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description