2LEG

Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.

Tang, M.Sperling, L.J.Berthold, D.A.Schwieters, C.D.Nesbitt, A.E.Nieuwkoop, A.J.Gennis, R.B.Rienstra, C.M.

(2011) J.Biomol.Nmr 51: 227-233

  • DOI: 10.1007/s10858-011-9565-6

  • PubMed Abstract: 
  • X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encro ...

    X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein DsbA
A
189Escherichia coli (strain K12)Gene Names: dsbA (dsf, ppfA)
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEG4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Disulfide bond formation protein B
B
176Escherichia coli (strain K12)Gene Names: dsbB (roxB, ycgA)
Find proteins for P0A6M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6M2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UQ1
Query on UQ1

Download SDF File 
Download CCD File 
B
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2LEG Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release