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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.44 kDa 
• Atom Count: 530 
• Modelled Residue Count: 71 
• Deposited Residue Count: 121 
• Unique protein chains: 1

6H5H

A computationally designed dRP lyase domain reconstructed from two heterologous fragments

• PDB DOI: 10.2210/pdb6H5H/pdb
• BMRB: 34304

• Classification: UNKNOWN FUNCTION
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-24 Released: 2018-12-12 
• Deposition Author(s): ElGamacy, M., Coles, M., Lupas, A.N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 22 
• Selection Criteria: structures with the least restraint violations 

Literature

Asymmetric protein design from conserved supersecondary structures.

ElGamacy, M., Coles, M., Lupas, A.

(2018) J Struct Biol 204: 380-387

• PubMed: 30558718 
• DOI: 10.1016/j.jsb.2018.10.010
• Primary Citation of Related Structures:  
  6H5H


• PubMed Abstract: 
  

Computational design with supersecondary structures as building blocks has proven effective in the construction of new proteins with controlled geometries. So far, this approach has primarily exploited amplification, effectively harnessing the internal folding propensity of self-compatible fragments to achieve sufficient enthalpy for folding. Here we exploit an interface-driven strategy to depart from the repeat design realm, constructing an asymmetric, globular domain from heterologous supersecondary structures. We report the successful design of a dRP lyase domain fold, which agrees with the experimental NMR structure at atomic accuracy (backbone RMSD of 0.94 Å). Our results show that the residual folding information within conserved fragments, combined with efficient interface-directed sampling, can effectively yield globular proteins with novel sequences and biophysical properties.

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Organizational Affiliation: 

Dept. of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polb4	A	121	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 22 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 6H5H Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-07-24 
• Released Date: 2018-12-12 
Deposition Author(s): ElGamacy, M., Coles, M., Lupas, A.N.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2018-12-26
  Changes: Data collection, Database references
• Version 1.2: 2019-05-08
  Changes: Data collection