7BPO | pdb_00007bpo

Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde

• PDB DOI: https://doi.org/10.2210/pdb7BPO/pdb

• Classification: LYASE
• Organism(s): Parafontaria falcifera
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-23 Released: 2021-03-24 
• Deposition Author(s): Nuylert, A., Nakabayashi, M., Yamaguchi, T., Asano, Y.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde

Nuylert, A., Nakabayashi, M., Yamaguchi, T., 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: 36.76 kDa 
• Atom Count: 3,041 
• Modeled Residue Count: 329 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A, B	165	Parafontaria falcifera	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.304	α = 90
b = 33.13	β = 106.17
c = 72.018	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Nuylert, A., Nakabayashi, M., Yamaguchi, T., Asano, Y.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER1102
Japan Society for the Promotion of Science (JSPS)	Japan	17H06169

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary