4KGS

Backbone Modifications in the Protein GB1 Loops: beta-3-Val21, beta-3-Asp40

• PDB DOI: https://doi.org/10.2210/pdb4KGS/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Streptococcus sp. group G
• Mutation(s): No 


• Deposited: 2013-04-29 Released: 2013-09-04 
• Deposition Author(s): Reinert, Z.E., Lengyel, G.A., Horne, W.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.217 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Protein-like Tertiary Folding Behavior from Heterogeneous Backbones.

Reinert, Z.E., Lengyel, G.A., Horne, W.S.

(2013) J Am Chem Soc 135: 12528-12531

• PubMed: 23937097 
• DOI: https://doi.org/10.1021/ja405422v
• Primary Citation of Related Structures:  
  4KGR, 4KGS, 4KGT


• PubMed Abstract: 
  

  Because proteins play vital roles in life, much effort has been invested in their mimicry by synthetic agents. One approach is to design unnatural backbone oligomers ("foldamers") that fold like natural peptides. Despite success in secondary structure mimicry by such species, protein-like tertiary folds remain elusive. A fundamental challenge underlying this task is the design of a sequence of side chains that will specify a complex tertiary folding pattern on an unnatural backbone. We report here a sequence-based approach to convert a natural protein with a compact tertiary fold to an analogue with a backbone composed of ~20% unnatural building blocks but folding behavior similar to that of the parent protein.

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Organizational Affiliation: 

Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.61 kDa 
• Atom Count: 1,003 
• Modelled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Val21, beta-3-Asp40	A, B	57	N/A	Mutation(s): 0
UniProt
Find proteins for P06654 (Streptococcus sp. group G) Explore P06654  Go to UniProtKB:  P06654

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3D	A, B	PEPTIDE-LIKE	C5 H9 N O4		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.217 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.657	α = 90
b = 35.66	β = 120.44
c = 46.531	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Reinert, Z.E., Lengyel, G.A., Horne, W.S.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations