4HJB | pdb_00004hjb

GCN4pLI derivative with alpha/beta/cyclic-gamma amino acid substitution pattern

• PDB DOI: https://doi.org/10.2210/pdb4HJB/pdb

• Classification: UNKNOWN FUNCTION
• Mutation(s): No 


• Deposited: 2012-10-12 Released: 2013-06-12 
• Deposition Author(s): Shin, Y.H., Mortenson, D.E., Satyshur, K.A., Forest, K.T., Gellman, S.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.191 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Differential Impact of beta and gamma Residue Preorganization on alpha / beta / gamma-Peptide Helix Stability in Water.

Shin, Y.H., Mortenson, D.E., Satyshur, K.A., Forest, K.T., Gellman, S.H.

(2013) J Am Chem Soc 135: 8149-8152

• PubMed: 23701135 
• DOI: https://doi.org/10.1021/ja403319q
• Primary Citation Related Structures: 
  4HJB, 4HJD


• PubMed Abstract: 
  

  Cyclic constraints have proven to be very effective for preorganizing β-amino acid residues and thereby stabilizing β- and α/β-peptide helices, but little is known about possible preorganization effects among γ residues. Here we assess and compare the impact of cyclic preorganization of β and γ residues in the context of a specific α/β/γ-peptide helix. The results show that β residue preorganization is critical for helix stability but that γ residue preorganization is less important.

---

Organizational Affiliation: 
• Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 15.97 kDa 
• Atom Count: 1,133 
• Modeled Residue Count: 124 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN4pLI(alpha/beta/cyclic-gamma)	A [auth C], B [auth A], C [auth B], D	33	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.191 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.19	α = 90
b = 46.29	β = 91.27
c = 34.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
EMBL	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Shin, Y.H., Mortenson, D.E., Satyshur, K.A., Forest, K.T., Gellman, S.H.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2014-02-19
  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
• Version 2.1: 2024-10-09
  Changes: Structure summary