3PEB | pdb_00003peb

The Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.

• PDB DOI: https://doi.org/10.2210/pdb3PEB/pdb

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


• Deposited: 2010-10-25 Released: 2010-11-03 
• Deposition Author(s): Cuff, M.E., Mack, J.C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

The Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.

Cuff, M.E., Mack, J.C., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.69 kDa 
• Atom Count: 1,327 
• Modeled Residue Count: 132 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidase	A	137	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: pepQ, stu0629
UniProt
Find proteins for Q5M567 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M567  Go to UniProtKB:  Q5M567

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.503	α = 90
b = 70.503	β = 90
c = 160.388	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Cuff, M.E., Mack, J.C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary