1JFR

CRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT 1.9A RESOLUTION: A MODEL FOR A FAMILY OF PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES

• PDB DOI:  https://doi.org/10.2210/pdb1JFR/pdb

• Classification: SERINE HYDROLASE
• Organism(s): Streptomyces exfoliatus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1997-07-11 Released: 1998-07-15 
• Deposition Author(s): Wei, Y., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.186 
• R-Value Work: 0.140 

Literature

Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution.

Wei, Y., Swenson, L., Castro, C., Derewenda, U., Minor, W., Arai, H., Aoki, J., Inoue, K., Servin-Gonzalez, L., Derewenda, Z.S.

(1998) Structure 6: 511-519

• PubMed: 9562561 
• DOI: https://doi.org/10.1016/s0969-2126(98)00052-5
• Primary Citation of Related Structures:  
  1JFR


• PubMed Abstract: 
  

  Neutral lipases are ubiquitous and diverse enzymes. The molecular architecture of the structurally characterized lipases is similar, often despite a lack of detectable homology at the sequence level. Some of the microbial lipases are evolutionarily related to physiologically important mammalian enzymes. For example, limited sequence similarities were recently noted for the Streptomyces exfoliatus lipase (SeL) and two mammalian platelet-activating factor acetylhydrolases (PAF-AHs). The determination of the crystal structure of SeL allowed us to explore the structure-function relationships in this novel family of homologous hydrolases.

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Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics, University of Virginia, Health Sciences Center, Charlottesville, VA 22906, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.93 kDa 
• Atom Count: 4,536 
• Modelled Residue Count: 520 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPASE	A, B	262	Streptomyces exfoliatus	Mutation(s): 0  Gene Names: STREPTOMYCES EXFOLIATUS Membrane Entity: Yes
UniProt
Find proteins for Q56008 (Streptomyces sp) Explore Q56008  Go to UniProtKB:  Q56008

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.186 
• R-Value Work: 0.140 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.5	α = 90
b = 53	β = 95.8
c = 81.1	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	data reduction
SHELX-90	model building
SHELX-90	refinement
CCP4	data scaling
SHELX-90	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-15 
Deposition Author(s): Wei, Y., Derewenda, Z.S.

Revision History  

• Version 1.0: 1998-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance