2LGI

Atomic Resolution Protein Structures using NMR Chemical Shift Tensors

Summary for 2LGI

• Entry DOI: 10.2210/pdb2lgi/pdb
• Related: 1GB1 1PGA 1PGB 2GB1 2GI9 2JSV 2JU6 2KOP 2KQ4 2KWD 2PLP 2QMT
• NMR Information: BMRB: 17810
• Descriptor: Immunoglobulin G-binding protein G (1 entity in total)
• Functional Keywords: gb1, immunoglobulin binding domain, tedor, protein binding, igg-binding protein, peptidoglycan-anchor, secreted, thermostable
• Biological source: Streptococcus sp. group G
• Cellular location: Secreted, cell wall; Peptidoglycan-anchor (Potential): P06654
• Total number of polymer chains: 1
• Total formula weight: 6228.81

Authors

Wylie, B.J.,Sperling, L.J.,Nieuwkoop, A.J.,Franks, W.T.,Oldfield, E.,Rienstra, C.M. (deposition date: 2011-07-26, release date: 2011-10-26, Last modification date: 2024-05-01)

Primary citation

Wylie, B.J.,Sperling, L.J.,Nieuwkoop, A.J.,Franks, W.T.,Oldfield, E.,Rienstra, C.M.
Ultrahigh resolution protein structures using NMR chemical shift tensors.
Proc.Natl.Acad.Sci.USA, 108:16974-16979, 2011

PubMed Abstract: NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for (13)Cα and (15)N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific (13)Cα and (15)N CSTs were measured using synchronously evolved recoupling experiments in which (13)C and (15)N tensors were projected onto the (1)H-(13)C and (1)H-(15)N vectors, respectively, and onto the (15)N-(13)C vector in the case of (13)Cα. The orientations of the (13)Cα CSTs to the (1)H-(13)C and (13)C-(15)N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured (15)N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the (15)N CST with respect to the (1)H-(15)N vector. Incorporation of the (13)Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance (13)C-(15)N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ(1)/χ(2) distributions, providing solid-state NMR with a powerful tool for de novo structure determination.

PubMed: 21969532
DOI: 10.1073/pnas.1103728108

Experimental method

SOLID-STATE NMR