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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q56008
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-07-15

Deposition Author(s):

Derewenda, Z.S.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.