9DK4 | pdb_00009dk4

ancestral hydroxynitrile lyase with fifteen substitutions

• PDB DOI: https://doi.org/10.2210/pdb9DK4/pdb

• Classification: LYASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-07 Released: 2024-10-02 
• Deposition Author(s): Sarak, S.C., Tan, P., Evans III, R.L., Shi, K., Kazlauskas, R.J., Aihara, H., Pierce, C.T., Walsh, M.E., Greenberg, L.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Ancestral hydroxynitrile lyase with fifteen substitutions

Tan, P., Sarak, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 124.29 kDa 
• Atom Count: 8,041 
• Modeled Residue Count: 994 
• Deposited Residue Count: 1,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fifteen-substitution variant of an ancestral hydroxynitrile lyase	A, B, C, D	272	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth B], H [auth C], I [auth C], J [auth D], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.244	α = 90
b = 80.385	β = 90.622
c = 92.823	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Sarak, S.C., Tan, P., Evans III, R.L., Shi, K., Kazlauskas, R.J., Aihara, H., Pierce, C.T., Walsh, M.E., Greenberg, L.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM118047
National Science Foundation (NSF, United States)	United States	CBET-2039039
Department of Energy (DOE, United States)	United States	DE-SC0012704
Department of Energy (DOE, United States)	United States	KP1605010
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Database references, Structure summary