Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.30 kDa 
• Atom Count: 443 
• Modelled Residue Count: 57 
• Deposited Residue Count: 57 
• Unique protein chains: 1

1FD6

DELTA0: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G

• PDB DOI: 10.2210/pdb1FD6/pdb
• BMRB: 5151

• Classification: PROTEIN BINDING
• Organism(s): Streptococcus sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-07-19 Released: 2001-09-19 
• Deposition Author(s): Ross, S.A., Sarisky, C.A., Su, A., Mayo, S.L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 40 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Literature

Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification.

Ross, S.A., Sarisky, C.A., Su, A., Mayo, S.L.

(2001) Protein Sci 10: 450-454

• PubMed: 11266631 
• DOI: 10.1110/ps.32501
• Primary Citation of Related Structures:  
  1FCL, 1FD6


• PubMed Abstract: 
  

The solution structures of two computationally designed core variants of the beta 1 domain of streptococcal protein G (G beta 1) were solved by (1)H NMR methods to assess the robustness of amino acid sequence selection by the ORBIT protein design package under changes in protein backbone specification. One variant has mutations at three of 10 core positions and corresponds to minimal perturbations of the native G beta 1 backbone. The other, with mutations at six of 10 positions, was calculated for a backbone in which the separation between G beta 1's alpha-helix and beta-sheet was increased by 15% relative to native G beta 1. Exchange broadening of some resonances and the complete absence of others in spectra of the sixfold mutant bespeak conformational heterogeneity in this protein. The NMR data were sufficiently abundant, however, to generate structures of similar, moderately high quality for both variants. Both proteins adopt backbone structures similar to their target folds. Moreover, the sequence selection algorithm successfully predicted all core chi(1) angles in both variants, five of six chi(2) angles in the threefold mutant and four of seven chi(2) angles in the sixfold mutant. We conclude that ORBIT calculates sequences that fold specifically to a geometry close to the template, even when the template is moderately perturbed relative to a naturally occurring structure. There are apparently limits to the size of acceptable perturbations: In this study, the larger perturbation led to undesired dynamic behavior.

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Organizational Affiliation: 

Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN G BINDING PROTEIN G	A	57	Streptococcus sp.	Mutation(s): 4
UniProt
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909  Go to UniProtKB:  P19909

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 40 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 
• OLDERADO: 1FD6 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-19 
• Released Date: 2001-09-19 
Deposition Author(s): Ross, S.A., Sarisky, C.A., Su, A., Mayo, S.L.

Revision History  

• Version 1.0: 2001-09-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations