8SNI

Hydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations

• PDB DOI: https://doi.org/10.2210/pdb8SNI/pdb

• Classification: LYASE
• Organism(s): Hevea brasiliensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-27 Released: 2024-02-28 
• Deposition Author(s): Walsh, M.E., Greenberg, L.R., Kazlauskas, R.J., Pierce, C.T., Aihara, H., Evans, R.L., Shi, K., Tan, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Hydroxynitrile Lyase from Hevea brasiliensis with Forty Mutations

Walsh, M.E., Greenberg, L.R.

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.

Macromolecule Content

• Total Structure Weight: 66.17 kDa 
• Atom Count: 4,098 
• Modelled Residue Count: 516 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-hydroxynitrile lyase	A, B	293	Hevea brasiliensis	Mutation(s): 38  Gene Names: HNL EC: 4.1.2.47
UniProt
Find proteins for P52704 (Hevea brasiliensis) Explore P52704  Go to UniProtKB:  P52704

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO (Subject of Investigation/LOI)	F [auth A], H [auth B]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4 (Subject of Investigation/LOI)	D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO (Subject of Investigation/LOI)	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.527	α = 90
b = 81.884	β = 90
c = 90.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Walsh, M.E., Greenberg, L.R., Kazlauskas, R.J., Pierce, C.T., Aihara, H., Evans, R.L., Shi, K., Tan, P.

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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	NIGMS R35-GM118047
National Science Foundation (NSF, United States)	United States	2039039

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release
  
• Version 2.0: 2025-02-19
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary