2LZE | pdb_00002lze

Ligase 10C

• PDB DOI: https://doi.org/10.2210/pdb2LZE/pdb
• BMRB: 18749

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


• Deposited: 2012-10-01 Released: 2012-10-24 
• Deposition Author(s): Chao, F., Morelli, A., Haugner, J., Churchfield, L., Hagmann, L., Shi, L., Masterson, L., Sarangi, R., Veglia, G., Seelig, B.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Structure and dynamics of a primordial catalytic fold generated by in vitro evolution.

Chao, F.A., Morelli, A., Iii, J.C., Churchfield, L., Hagmann, L.N., Shi, L., Masterson, L.R., Sarangi, R., Veglia, G., Seelig, B.

(2013) Nat Chem Biol 9: 81-83

• PubMed: 23222886 
• DOI: https://doi.org/10.1038/nchembio.1138
• Primary Citation Related Structures: 
  2LZE


• PubMed Abstract: 
  

  Engineering functional protein scaffolds capable of carrying out chemical catalysis is a major challenge in enzyme design. Starting from a noncatalytic protein scaffold, we recently generated a new RNA ligase by in vitro directed evolution. This artificial enzyme lost its original fold and adopted an entirely new structure with substantially enhanced conformational dynamics, demonstrating that a primordial fold with suitable flexibility is sufficient to carry out enzymatic function.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.93 kDa 
• Atom Count: 683 
• Modeled Residue Count: 87 
• Deposited Residue Count: 87 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
a primordial catalytic fold generated by in vitro evolution	A	87	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Chao, F., Morelli, A., Haugner, J., Churchfield, L., Hagmann, L., Shi, L., Masterson, L., Sarangi, R., Veglia, G., Seelig, B.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 1.2: 2012-12-26
  Changes: Database references
• Version 1.3: 2013-02-06
  Changes: Database references
• Version 1.4: 2024-05-01
  Changes: Data collection, Database references, Derived calculations