6CL4 | pdb_00006cl4

LipC12 - Lipase from metagenomics


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.251 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability.

Martini, V.P.Krieger, N.Glogauer, A.Souza, E.M.Iulek, J.

(2019) N Biotechnol 53: 65-72

  • DOI: https://doi.org/10.1016/j.nbt.2019.07.001
  • Primary Citation Related Structures: 
    6CL4

  • PubMed Abstract: 

    Metagenomics is a modern approach to discovery of new enzymes with novel properties. This article reports the structure of a new lipase, belonging to family I.1, obtained by means of metagenomics. Its structure presents a fold typical of α/β hydrolases, with the lid in closed conformation. The protein was previously shown to present high thermostability and to be stable in aqueous solutions of polar organic solvents at high concentrations [30% (V/V)]. Molecular dynamics studies showed that the protein maintains its structure well in organic solvents. They also suggested that its thermostability might be enhanced if it were mutated to present a disulfide bond similar to that typically found in lipase family I.2. These findings identify this lipase as a good candidate for further improvement through protein engineering.


  • Organizational Affiliation
    • Department of Chemistry, Federal University of Paraná, Rua Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-990, Brazil. Electronic address: viviane.martini@ifpr.edu.br.

Macromolecule Content 

  • Total Structure Weight: 33.43 kDa 
  • Atom Count: 2,353 
  • Modeled Residue Count: 290 
  • Deposited Residue Count: 313 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipase C12313uncultured bacteriumMutation(s): 0 
Gene Names: lipc12
EC: 3.1.1.3
UniProt
Find proteins for A0ACD6B8K3 (uncultured bacterium)
Explore A0ACD6B8K3 
Go to UniProtKB:  A0ACD6B8K3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8K3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.5α = 90
b = 58.5β = 90
c = 192.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description