1QYS | pdb_00001qys

Crystal structure of Top7: A computationally designed protein with a novel fold

• PDB DOI: https://doi.org/10.2210/pdb1QYS/pdb

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


• Deposited: 2003-09-11 Released: 2003-11-25 
• Deposition Author(s): Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., Baker, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.293 (Depositor), 0.337 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.286 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Literature

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., Baker, D.

(2003) Science 302: 1364-1368

• PubMed: 14631033 
• DOI: https://doi.org/10.1126/science.1089427
• Primary Citation of Related Structures:  
  1QYS


• PubMed Abstract: 
  

  A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.13 kDa 
• Atom Count: 692 
• Modeled Residue Count: 92 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOP7	A	106	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.293 (Depositor), 0.337 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.286 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.9	α = 90
b = 35.9	β = 90
c = 140.554	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-25 
Deposition Author(s): Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., Baker, D.

Revision History  

• Version 1.0: 2003-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary