2UZ1

1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-methyl- 2,4-pentanediol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Thdp-Dependent Enzyme Benzaldehyde Lyase Refined to 1.65 A Resolution.

Maraite, A.Schmidt, T.Ansorge-Schumacher, M.B.Brzozowski, A.M.Grogan, G.

(2007) Acta Crystallogr.,Sect.F 63: 546

  • DOI: 10.1107/S1744309107028576

  • PubMed Abstract: 
  • Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the in ...

    Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 A using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005), FEBS J. 272, 6067-6076]. In this communication of parallel studies, BAL was crystallized in an alternative space group (P2(1)2(1)2(1)) and its structure refined to a resolution of 1.65 A, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.


    Organizational Affiliation

    Department of Biotechnology, Faculty of Natural Sciences, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BENZALDEHYDE LYASE
A, D
563Pseudomonas fluorescensGene Names: bznB
Find proteins for Q9F4L3 (Pseudomonas fluorescens)
Go to UniProtKB:  Q9F4L3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BENZALDEHYDE LYASE
B, C
563Pseudomonas fluorescensGene Names: bznB
Find proteins for Q9F4L3 (Pseudomonas fluorescens)
Go to UniProtKB:  Q9F4L3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.462α = 90.00
b = 121.601β = 90.00
c = 162.957γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance