Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.55 kDa 
• Atom Count: 2575 
• Modelled Residue Count: 322 
• Deposited Residue Count: 365 
• Unique protein chains: 2

2LEG

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

• DOI: 10.2210/pdb2LEG/pdb
• BMRB: 17710

• Classification: MEMBRANE PROTEIN, OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2011-06-15 Released: 2011-10-26 
• Deposition Author(s): Tang, M., Sperling, L.J., Berthold, D.A., Schwieters, C.D., Nesbitt, A.E., Nieuwkoop, A.J., Gennis, R.B., Rienstra, C.M.

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Experimental Data Snapshot

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

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

• PubMed: 21938394 
• DOI: 10.1007/s10858-011-9565-6
• Primary Citation of Related Structures:  
  2LEG


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A	189	Escherichia coli K-12	Mutation(s): 1  Gene Names: dsbA, dsf, ppfA, b3860, JW3832 Membrane Entity: Yes
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Disulfide bond formation protein B	B	176	Escherichia coli K-12	Mutation(s): 3  Gene Names: dsbB, roxB, ycgA, b1185, JW5182 Membrane Entity: Yes
UniProt
Find proteins for P0A6M2 (Escherichia coli (strain K12)) Explore P0A6M2  Go to UniProtKB:  P0A6M2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UQ1 (Subject of Investigation/LOI)	D [auth B]	UBIQUINONE-1 C14 H18 O4 SOECUQMRSRVZQQ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Entry History 

Deposition Data

• Deposited Date: 2011-06-15 
• Released Date: 2011-10-26 
Deposition Author(s): Tang, M., Sperling, L.J., Berthold, D.A., Schwieters, C.D., Nesbitt, A.E., Nieuwkoop, A.J., Gennis, R.B., Rienstra, C.M.

Revision History  

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