7BID | pdb_00007bid

Crystal structure of v31WRAP-T, a 7-bladed designer protein

• PDB DOI: https://doi.org/10.2210/pdb7BID/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-01-12 Released: 2021-09-22 
• Deposition Author(s): Laier, I., Mylemans, B., Lee, X.Y., Voet, A.R.D.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Structure and stability of the designer protein WRAP-T and its permutants.

Mylemans, B., Lee, X.Y., Laier, I., Helsen, C., Voet, A.R.D.

(2021) Sci Rep 11: 18867-18867

• PubMed: 34552189 
• DOI: https://doi.org/10.1038/s41598-021-98391-0
• Primary Citation Related Structures: 
  7BID, 7BIE, 7BIF, 7BIG


• PubMed Abstract: 
  

  [Formula: see text]-Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats ('blades') each consisting of a 4-stranded anti-parallel [Formula: see text]-sheet. So far, 4- to 12-bladed [Formula: see text]-propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetric [Formula: see text]-propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to each [Formula: see text]-propeller sub-family.

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Organizational Affiliation: 
• Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium.
Laboratory of Molecular Endocrinology, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium.
Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.35 kDa 
• Atom Count: 2,479 
• Modeled Residue Count: 286 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
v31WRAP-T	A	291	synthetic construct	Mutation(s): 8
UniProt
Find proteins for B2J0I0 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J0I0  Go to UniProtKB:  B2J0I0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.636	α = 90
b = 61.396	β = 90
c = 99.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Laier, I., Mylemans, B., Lee, X.Y., Voet, A.R.D.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0E4717N
Research Foundation - Flanders (FWO)	Belgium	G0F9316N
Research Foundation - Flanders (FWO)	Belgium	G051917N
Research Foundation - Flanders (FWO)	Belgium	GBM-D3229-ASP/17

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description