1WQ2

Neutron Crystal Structure Of Dissimilatory Sulfite Reductase D (DsrD)


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Related Citations: 
    • Hydration structures in proteins and neutron diffraction experiment on dissimilatory sul te reductase D (DsrD)
      Chatake, T., Ostermann, A., Kurihara, K., Parak, F.G., Mizuno, N., Voordouw, G., Higuchi, Y., Tanaka, I., Niimura, N.
      (2004) J Synchrotron Radiat 11: 72

    Organizational Affiliation

    Neutron Structural Biology, Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein dsvDA, B78Desulfovibrio vulgarisMutation(s): 0 
UniProt
Find proteins for Q46582 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q46582 
Go to UniProtKB:  Q46582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46582
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.5α = 90
b = 65.1β = 90
c = 46.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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