2OXG | pdb_00002oxg

The SoxYZ Complex of Paracoccus pantotrophus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.194 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The SoxYZ Complex Carries Sulfur Cycle Intermediates on a Peptide Swinging Arm.

Sauve, V.Bruno, S.Berks, B.C.Hemmings, A.M.

(2007) J Biological Chem 282: 23194-23204

  • DOI: https://doi.org/10.1074/jbc.M701602200
  • Primary Citation Related Structures: 
    2OX5, 2OXG, 2OXH

  • PubMed Abstract: 

    The bacterial Sox (sulfur oxidizing) system allows the utilization of inorganic sulfur compounds in energy metabolism. Central to this process is the SoxYZ complex that carries the pathway intermediates on a cysteine residue near the C terminus of SoxY. Crystal structures have been determined for Paracoccus pantotrophus SoxYZ with the carrier cysteine in the underivatized state, conjugated to the polysulfide mimic beta-mercaptoethanol, and as the sulfonate adduct pathway intermediate. The carrier cysteine is located on a peptide swinging arm and is bracketed on either side by diglycine dipeptides acting as molecular universal joints. This structure provides a novel solution to the requirement that the cysteine-bound intermediates be able to access and orient themselves within the active sites of multiple partner enzymes. Adjacent to the swinging arm there is a conserved, deep, apolar pocket into which the beta-mercaptoethanol adduct extends. This pocket would be well suited to a role in protecting labile pathway intermediates from adventitious reactions.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 97.03 kDa 
  • Atom Count: 7,094 
  • Modeled Residue Count: 861 
  • Deposited Residue Count: 928 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SoxZ proteinA [auth Z],
C [auth A],
E [auth C],
G [auth E]
108Paracoccus denitrificansMutation(s): 0 
Gene Names: soxZ
UniProt
Find proteins for Q9LCU8 (Paracoccus denitrificans)
Explore Q9LCU8 
Go to UniProtKB:  Q9LCU8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCU8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SoxY proteinB [auth Y],
D [auth B],
F [auth D],
H [auth F]
124Paracoccus denitrificansMutation(s): 0 
Gene Names: soxY
UniProt
Find proteins for Q9LCU9 (Paracoccus denitrificans)
Explore Q9LCU9 
Go to UniProtKB:  Q9LCU9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCU9
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.194 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.828α = 90
b = 54.717β = 98.68
c = 77.677γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description