2UZ1 | pdb_00002uz1

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

PDB DOI: https://doi.org/10.2210/pdb2UZ1/pdb

Classification: LYASE
Organism(s): Pseudomonas fluorescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-04-23 Released: 2007-07-24
Deposition Author(s): Maraite, A., Schmidt, T., Ansorge-Schumacher, M.B., Brzozowski, A.M., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.192 (Depositor), 0.191 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 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 Struct Biol Cryst Commun 63: 546

PubMed: 17620706 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309107028576
Primary Citation Related Structures:
2UZ1

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 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.

Macromolecule Content

Total Structure Weight: 237.96 kDa
Atom Count: 18,289
Modeled Residue Count: 2,218
Deposited Residue Count: 2,252
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BENZALDEHYDE LYASE	A, D	563	Pseudomonas fluorescens	Mutation(s): 0 EC: 4.1.2.38
UniProt
Find proteins for Q9F4L3 (Pseudomonas fluorescens) Explore Q9F4L3 Go to UniProtKB: Q9F4L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9F4L3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BENZALDEHYDE LYASE	B, C	563	Pseudomonas fluorescens	Mutation(s): 0 EC: 4.1.2.38
UniProt
Find proteins for P51853 (Pseudomonas fluorescens) Explore P51853 Go to UniProtKB: P51853
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51853
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], F [auth B], I [auth C], K [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain K [auth D]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	G [auth B], H [auth B], J [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.192 (Depositor), 0.191 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.462	α = 90
b = 121.601	β = 90
c = 162.957	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

Maraite, A.

Schmidt, T.

Ansorge-Schumacher, M.B.

Brzozowski, A.M.

Grogan, G.

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description