5E6G | pdb_00005e6g

Crystal Structure of De Novo Designed Protein CA01

• PDB DOI: https://doi.org/10.2210/pdb5E6G/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-09 Released: 2016-05-18 
• Deposition Author(s): Jacobs, T.M., Williams, T., Kuhlman, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.234 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Design of structurally distinct proteins using strategies inspired by evolution.

Jacobs, T.M., Williams, B., Williams, T., Xu, X., Eletsky, A., Federizon, J.F., Szyperski, T., Kuhlman, B.

(2016) Science 352: 687-690

• PubMed: 27151863 
• DOI: https://doi.org/10.1126/science.aad8036
• Primary Citation Related Structures: 
  2N8I, 2N8W, 5E6G


• PubMed Abstract: 
  

  Natural recombination combines pieces of preexisting proteins to create new tertiary structures and functions. We describe a computational protocol, called SEWING, which is inspired by this process and builds new proteins from connected or disconnected pieces of existing structures. Helical proteins designed with SEWING contain structural features absent from other de novo designed proteins and, in some cases, remain folded at more than 100°C. High-resolution structures of the designed proteins CA01 and DA05R1 were solved by x-ray crystallography (2.2 angstrom resolution) and nuclear magnetic resonance, respectively, and there was excellent agreement with the design models. This method provides a new strategy to rapidly create large numbers of diverse and designable protein scaffolds.

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Organizational Affiliation: 
• Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA. Northeast Structural Genomics Consortium.
Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.44 kDa 
• Atom Count: 1,980 
• Modeled Residue Count: 227 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed protein CA01	A, B	136	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.234 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.537	α = 90
b = 116.537	β = 90
c = 57.215	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Jacobs, T.M., Williams, T., Kuhlman, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM073960

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references