1HQD | pdb_00001hqd

PSEUDOMONAS CEPACIA LIPASE COMPLEXED WITH TRANSITION STATE ANALOGUE OF 1-PHENOXY-2-ACETOXY BUTANE

• PDB DOI: https://doi.org/10.2210/pdb1HQD/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia cepacia
• Mutation(s): No 


• Deposited: 2000-12-15 Released: 2001-08-22 
• Deposition Author(s): Luic, M., Tomic, S., Lescic, I., Ljubovic, E., Sepac, D., Sunjic, V., Vitale, L., Saenger, W., Kojic-Prodic, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.203 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Complex of Burkholderia cepacia lipase with transition state analogue of 1-phenoxy-2-acetoxybutane: biocatalytic, structural and modelling study.

Luic, M., Tomic, S., Lescic, I., Ljubovic, E., Sepac, D., Sunjic, V., Vitale, L., Saenger, W., Kojic-Prodic, B.

(2001) Eur J Biochem 268: 3964-3973

• PubMed: 11453990 
• DOI: https://doi.org/10.1046/j.1432-1327.2001.02303.x
• Primary Citation Related Structures: 
  1HQD


• PubMed Abstract: 
  

  In a series of four racemic phenoxyalkyl-alkyl carbinols, 1-phenoxy-2-hydroxybutane (1) is enantioselectively acetylated by Burkholderia cepacia (formerly Pseudomonas cepacia) lipase with an E value > or = 200, whereas for the other three racemates E was found to be < or = 4. To explain the high preference of B. cepacia lipase for (R)-(+)-1, a precursor of its transition state analogue with a tetrahedral P-atom, (R(P),S(P))-O-(2R)-(1-phenoxybut-2-yl)methylphosphonic acid chloride was prepared and crystallized in complex with B. cepacia lipase. The X-ray structure of the complex was determined, allowing to compare the conformation of the inhibitor with results of molecular modelling.

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Organizational Affiliation: 
• Rudjer Boskovic Institute, Zagreb, Croatia] Institut für Chemie-Kristallographie, Freie Universität Berlin, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.45 kDa 
• Atom Count: 2,642 
• Modeled Residue Count: 320 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPASE	A	320	Burkholderia cepacia	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for P22088 (Burkholderia cepacia) Explore P22088  Go to UniProtKB:  P22088

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
INK	C [auth A]	(RP,SP)-O-(2R)-(1-PHENOXYBUT-2-YL)-METHYLPHOSPHONIC ACID CHLORIDE C11 H16 Cl O3 P YEIXDWIEYXZUBR-QLJPJBMISA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.203 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.06	α = 90
b = 46.63	β = 120.86
c = 84.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-08-22 
Deposition Author(s): Luic, M., Tomic, S., Lescic, I., Ljubovic, E., Sepac, D., Sunjic, V., Vitale, L., Saenger, W., Kojic-Prodic, B.

Revision History  

• Version 1.0: 2001-08-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary