6KFE

Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis (recombinant)

• PDB DOI: https://doi.org/10.2210/pdb6KFE/pdb

• Classification: LYASE
• Organism(s): Chamberlinius hualienensis
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-07-07 Released: 2020-07-08 
• Deposition Author(s): Motojima, F., Izumi, A., Asano, Y.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.157 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Functional and crystallographic analysis of hydroxynitrile lyase from the millipede, Chamberlinius hualienensis

Motojima, F., Izumi, A., Zhai, Z., Yamaguchi, T., Shichida, S., Nakano, S., Dadashipour, M., Asano, Y.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 18.8 kDa 
• Atom Count: 1,500 
• Modelled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A	162	Chamberlinius hualienensis	Mutation(s): 0  Gene Names: ChuaHNL
UniProt
Find proteins for A0A0H5BR52 (Chamberlinius hualienensis) Explore A0A0H5BR52  Go to UniProtKB:  A0A0H5BR52
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT	B [auth A], C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.205 
• R-Value Work: 0.157 
• R-Value Observed: 0.160 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.924	α = 90
b = 57.924	β = 90
c = 226.321	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Motojima, F., Izumi, A., Asano, Y.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER1102

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-13
  Changes: Structure summary