PDBsum entry 5bmh

Immune system

PDB id: 5bmh

Contents

Protein chain

56 a.a.

Ligands

MTN

Waters ×96

PDB id:

5bmh

Name:

Immune system

Title:

Nitroxide spin labels in protein gb1: t44 mutant, crystal form b

Structure:

Immunoglobulin g-binding protein g. Chain: a. Fragment: unp residues 304-357. Synonym: igg-binding protein g. Engineered: yes. Mutation: yes

Source:

Streptococcus sp. Group g. Organism_taxid: 1320. Gene: spg. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.60Å R-factor: 0.156 R-free: 0.175

Authors:

T.C.Cunningham,W.S.Horne,S.Saxena

Key ref:

T.F.Cunningham et al. (2016). Rotameric preferences of a protein spin label at edge-strand β-sheet sites. Protein Sci, 25, 1049-1060. PubMed id: 26948069 DOI: 10.1002/pro.2918

Date:

22-May-15 Release date: 06-Apr-16

Protein chain

P19909  (SPG2_STRSG) -  Immunoglobulin G-binding protein G from Streptococcus sp. group G

Seq: 593 a.a.

Struc: 56 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1002/pro.2918

Protein Sci 25:1049-1060 (2016)

PubMed id: 26948069

Rotameric preferences of a protein spin label at edge-strand β-sheet sites.

T.F.Cunningham, S.Pornsuwan, W.S.Horne, S.Saxena.

ABSTRACT

Protein spin labeling to yield the nitroxide-based R1 side chain is a powerful method to measure protein dynamics and structure by electron spin resonance. However, R1 measurements are complicated by the flexibility of the side chain. While analysis approaches for solvent-exposed α-helical environment have been developed to partially account for flexibility, similar work in β-sheets is lacking. The goal of this study is to provide the first essential steps for understanding the conformational preferences of R1 within edge β-strands using X-ray crystallography and double electron electron resonance (DEER) distance measurements. Crystal structures yielded seven rotamers for a non-hydrogen-bonded site and three rotamers for a hydrogen-bonded site. The observed rotamers indicate contextual differences in R1 conformational preferences compared to other solvent-exposed environments. For the DEER measurements, each strand site was paired with the same α-helical site elsewhere on the protein. The most probable distance observed by DEER is rationalized based on the rotamers observed in the crystal structure. Additionally, the appropriateness of common molecular modeling methods that account for R1 conformational preferences are assessed for the β-sheet environment. These results show that interpretation of R1 behavior in β-sheets is difficult and indicate further development is needed for these computational methods to correctly relate DEER distances to protein structure at edge β-strand sites.