3OOO | pdb_00003ooo

The structure of a proline dipeptidase from Streptococcus agalactiae 2603V

• PDB DOI: https://doi.org/10.2210/pdb3OOO/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus agalactiae 2603V/R
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-31 Released: 2010-09-22 
• Deposition Author(s): Fan, Y., Wu, R., Morales, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The structure of a proline dipeptidase from Streptococcus agalactiae 2603V

Fan, Y., Wu, R., Morales, J., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.79 kDa 
• Atom Count: 2,641 
• Modeled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline dipeptidase	A, B	132	Streptococcus agalactiae 2603V/R	Mutation(s): 0  Gene Names: pepQ, SAG0706
UniProt
Find proteins for Q8E0M4 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8E0M4  Go to UniProtKB:  Q8E0M4

Small Molecules

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: 1.57 Å
• R-Value Free:  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.744	α = 90
b = 58.325	β = 90
c = 101.995	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Fan, Y., Wu, R., Morales, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary