3IL0

The crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb3IL0/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-08-06 Released: 2009-09-08 
• Deposition Author(s): Zhang, R., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

The crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus

Zhang, R., Hatzos, C., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.59 kDa 
• Atom Count: 2,178 
• Modelled Residue Count: 256 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase P; XAA-pro aminopeptidase	A, B	131	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: GI:55737699, pepP, stu1742
UniProt
Find proteins for Q5M2R3 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M2R3  Go to UniProtKB:  Q5M2R3

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.303	α = 90
b = 80.396	β = 90
c = 100.858	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Zhang, R., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations