7BR1

Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde prepared by cocrystallization

Nuylert, A.Nakabayashi, M.Yamaguchi, T.Asano, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxynitrile lyase
A, B
164Parafontaria laminataMutation(s): 0 
UniProt
Find proteins for A0A7I6N400 (Parafontaria laminata)
Explore A0A7I6N400 
Go to UniProtKB:  A0A7I6N400
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7I6N400
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HBX (Subject of Investigation/LOI)
Query on HBX

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
benzaldehyde
C7 H6 O
HUMNYLRZRPPJDN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN (Subject of Investigation/LOI)
Query on SCN

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.934α = 90
b = 32.763β = 102.84
c = 84.632γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJER1102
Japan Society for the Promotion of Science (JSPS)Japan17H06169

Revision History  (Full details and data files)

  • 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