5U9U | pdb_00005u9u

De Novo Three-stranded Coiled Coil Peptide Containing a Tris-thiolate Site Engineered by D-Cysteine Ligands

• PDB DOI: https://doi.org/10.2210/pdb5U9U/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2016-12-18 Released: 2017-04-26 
• Deposition Author(s): Ruckthong, L., Stuckey, J.A., Pecoraro, V.L.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils.

Ruckthong, L., Peacock, A.F.A., Pascoe, C.E., Hemmingsen, L., Stuckey, J.A., Pecoraro, V.L.

(2017) Chemistry 23: 8232-8243

• PubMed: 28384393 
• DOI: https://doi.org/10.1002/chem.201700660
• Primary Citation Related Structures: 
  5U9T, 5U9U


• PubMed Abstract: 
  

  Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of Zn ^II Cl(CSL16 _D C) ₃ ^2- to the published structure of Zn ^II (H ₂ O)(GRAND-CSL12AL16 _L C) ₃ ^- . Moreover, spectroscopic analysis indicates that the Cd ^II geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate Cd ^II ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.

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Organizational Affiliation: 
• Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.
Present address: Department Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, ThungKhru, Bangkok, 10140, Thailand.
Present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark.
Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA.

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: 13.33 kDa 
• Atom Count: 904 
• Modeled Residue Count: 93 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apo-(CoilSer L16(DCY))3	A, B, C	31	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	H [auth B], J [auth C]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
ZN	D [auth A], E [auth B], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.327	α = 90
b = 67.517	β = 90
c = 69.034	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Ruckthong, L., Stuckey, J.A., Pecoraro, V.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES012236

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references, Refinement description
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary