Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.93 kDa 
• Atom Count: 1202 
• Modelled Residue Count: 119 
• Deposited Residue Count: 139 
• Unique protein chains: 1

3PFU

N-terminal domain of Thiol:disulfide interchange protein DsbD in its reduced form

• PDB DOI: 10.2210/pdb3PFU/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-29 Released: 2011-05-04 
• Deposition Author(s): Mavridou, D.A.I., Saridakis, E., Ferguson, S.J., Redfield, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Oxidation state-dependent protein-protein interactions in disulfide cascades

Mavridou, D.A., Saridakis, E., Kritsiligkou, P., Goddard, A.D., Stevens, J.M., Ferguson, S.J., Redfield, C.

(2011) J Biol Chem 286: 24943-24956

• PubMed: 21543317 
• DOI: 10.1074/jbc.M111.236141
• Primary Citation of Related Structures:  
  3PFU


• PubMed Abstract: 
  

Bacterial growth and pathogenicity depend on the correct formation of disulfide bonds, a process controlled by the Dsb system in the periplasm of Gram-negative bacteria. Proteins with a thioredoxin fold play a central role in this process. A general feature of thiol-disulfide exchange reactions is the need to avoid a long lived product complex between protein partners. We use a multidisciplinary approach, involving NMR, x-ray crystallography, surface plasmon resonance, mutagenesis, and in vivo experiments, to investigate the interaction between the two soluble domains of the transmembrane reductant conductor DsbD. Our results show oxidation state-dependent affinities between these two domains. These observations have implications for the interactions of the ubiquitous thioredoxin-like proteins with their substrates, provide insight into the key role played by a unique redox partner with an immunoglobulin fold, and are of general importance for oxidative protein-folding pathways in all organisms.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein dsbD	A	139	Escherichia coli K-12	Mutation(s): 0  Gene Names: dsbD, cutA2, cycZ, dipZ, b4136, JW5734 EC: 1.8.1.8
UniProt
Find proteins for P36655 (Escherichia coli (strain K12)) Explore P36655  Go to UniProtKB:  P36655

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	B [auth A], C [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.74	α = 90
b = 55.552	β = 90
c = 105.209	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-29 
• Released Date: 2011-05-04 
Deposition Author(s): Mavridou, D.A.I., Saridakis, E., Ferguson, S.J., Redfield, C.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-05-15
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description