1DMS

STRUCTURE OF DMSO REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of dimethyl sulfoxide reductase from Rhodobacter capsulatus at 1.88 A resolution.

Schneider, F.Lowe, J.Huber, R.Schindelin, H.Kisker, C.Knablein, J.

(1996) J.Mol.Biol. 263: 53-69

  • DOI: 10.1006/jmbi.1996.0555

  • PubMed Abstract: 
  • The periplasmic dimethyl sulfoxide reductase (DMSOR) from the photosynthetic purple bacterium Rhodobacter capsulatus functions as the terminal electron acceptor in its respiratory chain. The enzyme catalyzes the reduction of highly oxidized substrate ...

    The periplasmic dimethyl sulfoxide reductase (DMSOR) from the photosynthetic purple bacterium Rhodobacter capsulatus functions as the terminal electron acceptor in its respiratory chain. The enzyme catalyzes the reduction of highly oxidized substrates like dimethyl sulfoxide to dimethyl sulfide. At a molybdenum redox center, two single electrons are transferred from cytochrome C556 to the substrate dimethyl sulfoxide, generating dimethyl sulfide and (with two protons) water. The enzyme was purified and crystallized in space group P4(1)2(1)2 with unit cell dimensions of a = b = 80.7 A and c = 229.2 A. The crystals diffract beyond 1.8 A with synchrotron radiation. The three-dimensional structure was solved by a combination of multiple isomorphous replacement and molecular replacement techniques. The atomic model was refined to an R-factor of 0.169 for 57,394 independent reflections. The spherical protein consists of four domains with a funnel-like cavity that leads to the freely accessible metal-ion redox center. The bis(molybdopterin guanine dinucleotide) molybdenum cofactor (1541 Da) of the single chain protein (85,033 Da) has the molybdenum ion bound to the cis-dithiolene group of only one molybdopterin guanine dinucleotide molecule. Three additional ligands, two oxo groups and the oxygen of a serine side-chain, are bound to the molybdenum ion. The second molybdopterin system is not part of the ligand sphere of the metal center with its sulfur atoms at distances of 3.5 A and 3.8 A away. It might be involved in electron shuttling from the protein surface to the molybdenum center.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, FRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DMSO REDUCTASE
A
781Rhodobacter capsulatusMutation(s): 0 
Gene Names: dorA
EC: 1.7.2.3, 1.8.5.3
Find proteins for Q52675 (Rhodobacter capsulatus)
Go to UniProtKB:  Q52675
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2MO
Query on 2MO

Download SDF File 
Download CCD File 
A
MOLYBDENUM (IV)OXIDE
Mo O2
QXYJCZRRLLQGCR-OMUOWVJPAU
 Ligand Interaction
PGD
Query on PGD

Download SDF File 
Download CCD File 
A
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H24 N10 O13 P2 S2
SOFMTHSWCZNJTQ-ILXWUORBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.700α = 90.00
b = 80.700β = 90.00
c = 229.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
MOSFLMdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-03-06
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2018-03-14
    Type: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary