1JI3 | pdb_00001ji3

CRYSTAL STRUCTURE OF THE FIRST THERMOSTABLE BACTERIAL LIPASE FROM BACILLUS STEAROTHERMOPHILUS

• PDB DOI: https://doi.org/10.2210/pdb1JI3/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-06-29 Released: 2002-11-01 
• Deposition Author(s): Tyndall, J.D.A., Sinchaikul, S., Fothergill-Gilmore, L.A., Taylor, P., Walkinshaw, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.210 (Depositor) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal Structure of a Thermostable Lipase from Bacillus stearothermophilus P1

Tyndall, J.D.A., Sinchaikul, S., Fothergill-Gilmore, L.A., Taylor, P., Walkinshaw, M.D.

(2002) J Mol Biology 323: 859-869

• PubMed: 12417199 
• DOI: https://doi.org/10.1016/s0022-2836(02)01004-5
• Primary Citation Related Structures: 
  1JI3


• PubMed Abstract: 
  

  We describe the first lipase structure from a thermophilic organism. It shares less than 20% amino acid sequence identity with other lipases for which there are crystal structures, and shows significant insertions compared with the typical alpha/beta hydrolase canonical fold. The structure contains a zinc-binding site which is unique among all lipases with known structures, and which may play a role in enhancing thermal stability. Zinc binding is mediated by two histidine and two aspartic acid residues. These residues are present in comparable positions in the sequences of certain lipases for which there is as yet no crystal structural information, such as those from Staphylococcal species and Arabidopsis thaliana. The structure of Bacillus stearothermophilus P1 lipase provides a template for other thermostable lipases, and offers insight into mechanisms used to enhance thermal stability which may be of commercial value in engineering lipases for industrial uses.

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Organizational Affiliation: 
• Structural Biochemistry Group, Institute of Cell and Molecular Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Scotland, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 86.83 kDa 
• Atom Count: 6,470 
• Modeled Residue Count: 776 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lipase	A, B	388	Geobacillus stearothermophilus	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for Q9L6D3 (Geobacillus stearothermophilus) Explore Q9L6D3  Go to UniProtKB:  Q9L6D3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.210 (Depositor) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.5	α = 90
b = 81.237	β = 96.33
c = 99.782	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-01 
Deposition Author(s): Tyndall, J.D.A., Sinchaikul, S., Fothergill-Gilmore, L.A., Taylor, P., Walkinshaw, M.D.

Revision History  

• Version 1.0: 2002-11-01
  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: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations