6LJI | pdb_00006lji

X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V

• PDB DOI: https://doi.org/10.2210/pdb6LJI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Streptococcus sp. 'group G
• Mutation(s): Yes 


• Deposited: 2019-12-16 Released: 2020-08-12 
• Deposition Author(s): Penmatsa, A., Chatterjee, J., Majumder, P., Khatri, B.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.328 (Depositor), 0.327 (DCC) 
• R-Value Work: 
  0.278 (Depositor), 0.281 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Model: experimental

Literature

Increasing protein stability by engineering the n -> pi * interaction at the beta-turn.

Khatri, B., Majumder, P., Nagesh, J., Penmatsa, A., Chatterjee, J.

(2020) Chem Sci 11: 9480-9487

• PubMed: 34094214 
• DOI: https://doi.org/10.1039/d0sc03060k
• Primary Citation Related Structures: 
  6L91, 6L9B, 6L9D, 6LJI


• PubMed Abstract: 
  

  Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction.

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Organizational Affiliation: 
• Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India [e-mail] [e-mail].
Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.31 kDa 
• Atom Count: 893 
• Modeled Residue Count: 112 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein G	A, B	56	Streptococcus sp. 'group G	Mutation(s): 2
UniProt
Find proteins for P06654 (Streptococcus sp. group G) Explore P06654  Go to UniProtKB:  P06654

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.328 (Depositor), 0.327 (DCC) 
• R-Value Work:  0.278 (Depositor), 0.281 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.722	α = 90
b = 23.066	β = 109.04
c = 48.395	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Penmatsa, A., Chatterjee, J., Majumder, P., Khatri, B.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	EMR/2016/006193
Department of Science & Technology (DST, India)	India	IR/SO/LU/0003/2010-PHASE-II

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2021-08-04
  Changes: Database references
• Version 1.2: 2022-02-09
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary