4L9A

Crystal structure of Smu.1393c from cariogenic pathogen Streptococcus mutans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and functional characterization of a novel alpha / beta hydrolase from cariogenic pathogen Streptococcus mutans

Wang, Z.Li, L.Su, X.-D.

(2013) Proteins --: --

  • DOI: 10.1002/prot.24418

  • PubMed Abstract: 
  • The protein Smu.1393c from Streptococcus mutans is annotated as a putative α/β hydrolase, but it has low sequence identity to the structure-known α/β hydrolases. Here we present the crystal structure of Smu.1393c at 2.0 Å resolution. Smu.1393c has a ...

    The protein Smu.1393c from Streptococcus mutans is annotated as a putative α/β hydrolase, but it has low sequence identity to the structure-known α/β hydrolases. Here we present the crystal structure of Smu.1393c at 2.0 Å resolution. Smu.1393c has a fully open alkaline substrate pocket, whose conformation is unique among other similar hydrolase structures. Three residues, Ser101, His251, and Glu125, were identified as the active center of Smu.1393c. By screening a series of artificial hydrolase substrates, we demonstrated Smu.1393c had low carboxylesterase activity towards short-chain carboxyl esters, which provided a clue for exploring the in vivo function of Smu.1393c.


    Organizational Affiliation

    State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein Smu.1393c
A, B
292Streptococcus mutans serotype c (strain ATCC 700610 / UA159)N/A
Find proteins for Q8DTF4 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Go to UniProtKB:  Q8DTF4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.504α = 90.00
b = 135.958β = 92.51
c = 51.568γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-18 
  • Released Date: 2013-07-17 
  • Deposition Author(s): Wang, Z., Li, L., Su, X.-D.
  • This entry supersedes: 3L80

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Database references