Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.00 kDa 
• Atom Count: 1128 
• Modelled Residue Count: 142 
• Deposited Residue Count: 142 
• Unique protein chains: 1

2KYI

Solution NMR structure of Dsy0195(21-82) protein from Desulfitobacterium Hafniense. Northeast Structural Genomics Consortium Target DhR8C

• PDB DOI: 10.2210/pdb2KYI/pdb
• BMRB: 16961

• Classification: Structural Genomics, Unknown function
• Organism(s): Desulfitobacterium hafniense Y51
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-27 Released: 2010-06-09 
• Deposition Author(s): Yang, Y., Ramelot, T.A., Cort, J.R., Wang, H., Ciccosanti, C., Foote, E.L., Jiang, M., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Combining NMR and EPR methods for homodimer protein structure determination.

Yang, Y., Ramelot, T.A., McCarrick, R.M., Ni, S., Feldmann, E.A., Cort, J.R., Wang, H., Ciccosanti, C., Jiang, M., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A.

(2010) J Am Chem Soc 132: 11910-11913

• PubMed: 20698532 
• DOI: 10.1021/ja105080h
• Primary Citation of Related Structures:  
  2KS0, 2KYI


• PubMed Abstract: 
  

There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 A. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	71	Desulfitobacterium hafniense Y51	Mutation(s): 0  Gene Names: DSY0195
UniProt
Find proteins for Q251Q8 (Desulfitobacterium hafniense (strain Y51)) Explore Q251Q8  Go to UniProtKB:  Q251Q8

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KYI Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-27 
• Released Date: 2010-06-09 
Deposition Author(s): Yang, Y., Ramelot, T.A., Cort, J.R., Wang, H., Ciccosanti, C., Foote, E.L., Jiang, M., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Other