3FRL | pdb_00003frl

The 2.25 A crystal structure of LipL32, the major surface antigen of Leptospira interrogans serovar Copenhageni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.227 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure and calcium-binding activity of LipL32, the major surface antigen of pathogenic Leptospira sp.

Hauk, P.Guzzo, C.R.Roman Ramos, H.Ho, P.L.Farah, C.S.

(2009) J Mol Biology 390: 722-736

  • DOI: https://doi.org/10.1016/j.jmb.2009.05.034
  • Primary Citation Related Structures: 
    3FRL

  • PubMed Abstract: 

    Leptospirosis, a spirochaetal zoonotic disease caused by Leptospira, has been recognized as an important emerging infectious disease. LipL32 is the major exposed outer membrane protein found exclusively in pathogenic leptospires, where it accounts for up to 75% of the total outer membrane proteins. It is highly immunogenic, and recent studies have implicated LipL32 as an extracellular matrix binding protein, interacting with collagens, fibronectin, and laminin. In order to better understand the biological role and the structural requirements for the function of this important lipoprotein, we have determined the 2.25-A-resolution structure of recombinant LipL32 protein corresponding to residues 21-272 of the wild-type protein (LipL32(21-272)). The LipL32(21-272) monomer is made of a jelly-roll fold core from which several peripheral secondary structures protrude. LipL32(21-272) is structurally similar to several other jelly-roll proteins, some of which bind calcium ions and extracellular matrix proteins. Indeed, spectroscopic data (circular dichroism, intrinsic tryptophan fluorescence, and extrinsic 1-amino-2-naphthol-4-sulfonic acid fluorescence) confirmed the calcium-binding properties of LipL32(21-272). Ca(2+) binding resulted in a significant increase in the thermal stability of the protein, and binding was specific for Ca(2+) as no structural or stability perturbations were observed for Mg(2+), Zn(2+), or Cu(2+). Careful examination of the crystallographic structure suggests the locations of putative regions that could mediate Ca(2+) binding as well as binding to other interacting host proteins, such as collagens, fibronectin, and laminin.


  • Organizational Affiliation
    • Centro de Biotecnologia, Instituto Butantan, SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 56 kDa 
  • Atom Count: 3,919 
  • Modeled Residue Count: 463 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LipL32
A, B
252Leptospira interrogans serovar CopenhageniMutation(s): 0 
Gene Names: LIC11352LIC_11352lipL32
UniProt
Find proteins for Q72SM7 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130))
Explore Q72SM7 
Go to UniProtKB:  Q72SM7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72SM7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.227 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.725α = 90
b = 126.725β = 90
c = 95.996γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary