3W92

Crystal Structure Analysis of the synthetic GCN4 Thioester coiled coil peptide

• PDB DOI: https://doi.org/10.2210/pdb3W92/pdb

• Classification: TRANSCRIPTION
• Mutation(s): No 


• Deposited: 2013-03-24 Released: 2014-02-12 
• Deposition Author(s): Shahar, A., Zarivach, R., Ashkenasy, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.190 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

A high-resolution structure that provides insight into coiled-coil thiodepsipeptide dynamic chemistry

Dadon, Z., Samiappan, M., Shahar, A., Zarivach, R., Ashkenasy, G.

(2013) Angew Chem Int Ed Engl 52: 9944-9947

• PubMed: 23929823 
• DOI: https://doi.org/10.1002/anie.201303900
• Primary Citation of Related Structures:  
  3W8V, 3W92, 3W93


• PubMed Abstract: 
  

  Stable and reactive: A crystal structure at 1.35 Å of a thioester coiled-coil protein reveals high similarity to all-peptide-bond proteins. In these assemblies, the thioester bonds are kept reactive towards thiol molecules in the mixture. This enables efficient domain exchange between proteins in response to changes in folding conditions or introduction of external templates.

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Organizational Affiliation: 

Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 84105 (Israel).

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 11.95 kDa 
• Atom Count: 1,003 
• Modelled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioester coiled coil peptide	A, B, C	32	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYZ	D [auth A], E [auth A], I [auth B], J [auth B], K [auth C]	PARA ACETAMIDO BENZOIC ACID C9 H9 N O3 QCXJEYYXVJIFCE-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth A], L [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.190 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.76	α = 90
b = 33.552	β = 90
c = 94.998	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Shahar, A., Zarivach, R., Ashkenasy, G.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations