2P6J | pdb_00002p6j

Full-sequence computational design and solution structure of a thermostable protein variant

• PDB DOI: https://doi.org/10.2210/pdb2P6J/pdb
• BMRB: 7401

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


• Deposited: 2007-03-18 Released: 2007-08-14 
• Deposition Author(s): Shah, P.S., Hom, G.K., Ross, S.A., Lassila, J.K., Crowhurst, K.A., Mayo, S.L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 43 
• Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 

Literature

Full-sequence Computational Design and Solution Structure of a Thermostable Protein Variant.

Shah, P.S., Hom, G.K., Ross, S.A., Lassila, J.K., Crowhurst, K.A., Mayo, S.L.

(2007) J Mol Biology 372: 1-6

• PubMed: 17628593 
• DOI: https://doi.org/10.1016/j.jmb.2007.06.032
• Primary Citation Related Structures: 
  2P6J


• PubMed Abstract: 
  

  Computational protein design procedures were applied to the redesign of the entire sequence of a 51 amino acid residue protein, Drosophila melanogaster engrailed homeodomain. Various sequence optimization algorithms were compared and two resulting designed sequences were experimentally evaluated. The two sequences differ by 11 mutations and share 22% and 24% sequence identity with the wild-type protein. Both computationally designed proteins were considerably more stable than the naturally occurring protein, with midpoints of thermal denaturation greater than 99 degrees C. The solution structure was determined for one of the two sequences using multidimensional heteronuclear NMR spectroscopy, and the structure was found to closely match the original design template scaffold.

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Organizational Affiliation: 
• Biochemistry and Molecular Biophysics Option, MC 114-96, California Institute of Technology, Pasadena, CA 91125, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.61 kDa 
• Atom Count: 466 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed engrailed homeodomain variant UVF	A	52	unidentified	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 43 
• Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Shah, P.S., Hom, G.K., Ross, S.A., Lassila, J.K., Crowhurst, K.A., Mayo, S.L.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations
• Version 1.3: 2024-05-22
  Changes: Data collection