3FNB | pdb_00003fnb

Crystal structure of acylaminoacyl peptidase SMU_737 from Streptococcus mutans UA159

• PDB DOI: https://doi.org/10.2210/pdb3FNB/pdb

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


• Deposited: 2008-12-23 Released: 2009-01-06 
• Deposition Author(s): Kim, Y., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.225 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of acylaminoacyl-peptidase SMU_737 from Streptococcus mutans UA159

Kim, Y., Hatzos, C., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.09 kDa 
• Atom Count: 6,379 
• Modelled Residue Count: 745 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylaminoacyl peptidase SMU_737	A, B	405	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: SMU_737
UniProt
Find proteins for Q8DUZ1 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DUZ1  Go to UniProtKB:  Q8DUZ1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth A], I [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
BME	D [auth A], H [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	F [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.12 Å
• R-Value Free:  0.225 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.832	α = 90
b = 56.468	β = 93.86
c = 99.901	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Kim, Y., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary