6COG | pdb_00006cog

AtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,A209I with benzaldehyde

• PDB DOI: https://doi.org/10.2210/pdb6COG/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-03-12 Released: 2019-03-20 
• Deposition Author(s): Jones, B.J., Kazlauskas, R.J., Desrouleaux, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.194 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

AtHNL enantioselectivity mutants

Jones, B.J., Desrouleaux, R., Kazlauskas, R.J.

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 Evidence: homology

Macromolecule Content 

• Total Structure Weight: 59.42 kDa 
• Atom Count: 4,481 
• Modeled Residue Count: 518 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-hydroxynitrile lyase	A, B	260	Arabidopsis thaliana	Mutation(s): 6  Gene Names: HNL, MES5, At5g10300, F18D22_70 EC: 4.1.2.10
UniProt
Find proteins for Q9LFT6 (Arabidopsis thaliana) Explore Q9LFT6  Go to UniProtKB:  Q9LFT6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBX (Subject of Investigation/LOI)	F [auth A], H [auth B]	benzaldehyde C7 H6 O HUMNYLRZRPPJDN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.194 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.772	α = 90
b = 87.002	β = 90
c = 122.775	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Jones, B.J., Kazlauskas, R.J., Desrouleaux, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM102205

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description