5HG2

Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35

• PDB DOI: https://doi.org/10.2210/pdb5HG2/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Streptococcus sp. 'group G
• Mutation(s): Yes 


• Deposited: 2016-01-07 Released: 2016-02-24 
• Deposition Author(s): Tavenor, N.A., Reinert, Z.E., Lengyel, G.A., Griffith, B.D., Horne, W.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Comparison of design strategies for alpha-helix backbone modification in a protein tertiary fold.

Tavenor, N.A., Reinert, Z.E., Lengyel, G.A., Griffith, B.D., Horne, W.S.

(2016) Chem Commun (Camb) 52: 3789-3792

• PubMed: 26853882 
• DOI: https://doi.org/10.1039/c6cc00273k
• Primary Citation of Related Structures:  
  5HFY, 5HG2, 5HI1


• PubMed Abstract: 
  

  We report here the comparison of five classes of unnatural amino acid building blocks for their ability to be accommodated into an α-helix in a protein tertiary fold context. High-resolution structural characterization and analysis of folding thermodynamics yield new insights into the relationship between backbone composition and folding energetics in α-helix mimetics and suggest refined design rules for engineering the backbones of natural sequences.

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Organizational Affiliation: 

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA. [e-mail].

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.34 kDa 
• Atom Count: 2,066 
• Modelled Residue Count: 228 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein G	A, B, C, D	57	Streptococcus sp. 'group G	Mutation(s): 1
UniProt
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909  Go to UniProtKB:  P19909

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth C], G [auth D], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3A	A, B, C, D	L-PEPTIDE LINKING	C4 H9 N O2		ALA
B3K	A, B, C, D	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.947	α = 90
b = 51.947	β = 90
c = 96.404	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Tavenor, N.A., Reinert, Z.E., Lengyel, G.A., Griffith, B.D., Horne, W.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107161

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2016-07-27
  Changes: Data collection
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations