4YK7 | pdb_00004yk7

Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu)

• PDB DOI: https://doi.org/10.2210/pdb4YK7/pdb

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


• Deposited: 2015-03-04 Released: 2016-04-13 
• Deposition Author(s): Dadashipour, M., Nakano, S., Asano, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.262 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu)

Dadashipour, M., Nakano, S., Asano, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.53 kDa 
• Atom Count: 8,348 
• 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
(S)-hydroxynitrile lyase	A, B, C, D	258	Manihot esculenta	Mutation(s): 1  Gene Names: HNL EC: 4.1.2.47
UniProt
Find proteins for P52705 (Manihot esculenta) Explore P52705  Go to UniProtKB:  P52705

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.262 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.469	α = 90
b = 88.098	β = 90
c = 135.213	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Dadashipour, M., Nakano, S., Asano, Y.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Refinement description