7BR1 | pdb_00007br1

Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization

• PDB DOI: https://doi.org/10.2210/pdb7BR1/pdb

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


• Deposited: 2020-03-26 Released: 2021-04-07 
• 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: 1.25 Å
• R-Value Free: 
  0.147 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde prepared by cocrystallization

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: 37.03 kDa 
• Atom Count: 3,105 
• Modeled Residue Count: 327 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A, B	164	Parafontaria laminata	Mutation(s): 0
UniProt
Find proteins for A0A7I6N400 (Parafontaria laminata) Explore A0A7I6N400  Go to UniProtKB:  A0A7I6N400

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBX (Subject of Investigation/LOI)	C [auth A], D [auth A], H [auth B], I [auth B]	benzaldehyde C7 H6 O HUMNYLRZRPPJDN-UHFFFAOYSA-N
EDO	G [auth A], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN (Subject of Investigation/LOI)	E [auth A], F [auth A], J [auth B], K [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.147 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.934	α = 90
b = 32.763	β = 102.84
c = 84.632	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: 2021-04-07 
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: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Source and taxonomy, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary