4OZA

Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36

• PDB DOI: https://doi.org/10.2210/pdb4OZA/pdb

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


• Deposited: 2014-02-14 Released: 2014-07-16 
• Deposition Author(s): Reinert, Z.E., Horne, W.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.260 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Folding Thermodynamics of Protein-Like Oligomers with Heterogeneous Backbones.

Reinert, Z.E., Horne, W.S.

(2014) Chem Sci 5: 3325-3330

• PubMed: 25071931 
• DOI: https://doi.org/10.1039/C4SC01094A
• Primary Citation of Related Structures:  
  4OZA, 4OZB, 4OZC


• PubMed Abstract: 
  

  The thermodynamics of protein folding are dictated by a complex interplay of interatomic interactions and physical forces. A variety of unnatural protein-like oligomers have the capacity to manifest defined folding patterns. While the energetics of folding in natural proteins is well studied, little is known about the forces that govern folding in modified backbones. Here, we explore the thermodynamic consequences of backbone alteration on protein folding, focusing on two types of chemical changes made in different structural contexts of a compact tertiary fold. Our results reveal a surprising favorable impact on folding entropy that accompanies modifications that increase disorder in the ensemble of unfolded states, due to differences in the solvation of natural and unnatural backbones.

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Organizational Affiliation: 

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15217, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 6.3 kDa 
• Atom Count: 489 
• Modelled Residue Count: 57 
• Deposited Residue Count: 57 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptococcal Protein GB1 Backbone Modified Variant: beta-3-Ala24, beta-3-Lys28, beta-3-Gln32, beta-3-Asp36	A	57	Streptococcus sp.	Mutation(s): 0
UniProt
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909  Go to UniProtKB:  P19909

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3A	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
B3D	A	L-PEPTIDE LINKING	C5 H9 N O4		ASP
B3K	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.260 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.944	α = 90
b = 65.944	β = 90
c = 21.896	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CrystalClear	phasing
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Reinert, Z.E., Horne, W.S.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2014-12-24
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.4: 2018-03-21
  Changes: Data collection
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-07-10
  Changes: Data collection