8J82 | pdb_00008j82

GaHNL-12gen (artificial S-hydroxynitrile lyase generated by GAOptimizer)

• PDB DOI: https://doi.org/10.2210/pdb8J82/pdb

• Classification: LYASE
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2023-04-29 Released: 2024-04-03 
• Deposition Author(s): Ozawa, H., Unno, I., Sekine, R., Ito, S., Nakano, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Development of evolutionary algorithm-based protein redesign method

Ozawa, H., Unno, I., Sekine, R., Chisuga, T., Ito, S., Nakano, S.

(2024) Cell Rep Phys Sci 5

• DOI: https://doi.org/10.1016/j.xcrp.2023.101758

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 122.17 kDa 
• Atom Count: 9,983 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-hydroxynitrile lyase	A, B, C, D	266	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.744	α = 90
b = 86.398	β = 90
c = 135.038	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Ozawa, H., Unno, I., Sekine, R., Ito, S., Nakano, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K14391
Japan Society for the Promotion of Science (JSPS)	Japan	21K05395
Japan Science and Technology	Japan	JPMJPR20AB

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release