3RKS | pdb_00003rks

Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) K176P mutant

• PDB DOI: https://doi.org/10.2210/pdb3RKS/pdb

• Classification: LYASE
• Organism(s): Manihot esculenta
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-04-18 Released: 2012-06-20 
• Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Dadashipour, M., Suzuki, A., Mizushima, T., Komeda, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystallographic Studies of Manihot esculenta hydroxynitrile lyase Lysine-to-Proline mutants

Cielo, C.B.C., Yamane, T., Asano, Y., Dadashipour, M., Suzuki, A., Mizushima, T., Komeda, H.

To be published.

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 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: 117.69 kDa 
• Atom Count: 8,807 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrilase	A, B, C, D	258	Manihot esculenta	Mutation(s): 1  Gene Names: HNL EC: 4.1.2.37 (PDB Primary Data), 4.1.2.47 (UniProt)
UniProt
Find proteins for P52705 (Manihot esculenta) Explore P52705  Go to UniProtKB:  P52705

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth C], F [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.628	α = 90
b = 91.414	β = 90
c = 137.441	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Dadashipour, M., Suzuki, A., Mizushima, T., Komeda, H.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations