4L9A | pdb_00004l9a

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

• PDB DOI: https://doi.org/10.2210/pdb4L9A/pdb
• Entry: 4L9A supersedes: 3L80

• Classification: HYDROLASE
• Organism(s): Streptococcus mutans UA159
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

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

Wang, Z., Li, L., Su, X.D.

(2014) Proteins 82: 695-700

• PubMed: 24115105 
• DOI: https://doi.org/10.1002/prot.24418
• Primary Citation of Related Structures:  
  4L9A


• 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 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.

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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.

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.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.98 kDa 
• Atom Count: 4,600 
• Modeled Residue Count: 537 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein Smu.1393c	A, B	292	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: SMU_1393c
UniProt
Find proteins for Q8DTF4 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTF4  Go to UniProtKB:  Q8DTF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.504	α = 90
b = 135.958	β = 92.51
c = 51.568	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary