4PV4

Proline aminopeptidase P II from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb4PV4/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-14 Released: 2014-04-02 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.198 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Proline aminopeptidase P II from Yersinia pestis

Osipiuk, J., Maltseva, N., Shatsman, S., Anderson, W.F., 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: 101.06 kDa 
• Atom Count: 8,426 
• Modelled Residue Count: 872 
• Deposited Residue Count: 890 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline aminopeptidase P II	A, B	445	Yersinia pestis	Mutation(s): 0  Gene Names: pepP, pepP2, y3297, YPO0910, YP_3607 EC: 3.4.11.9
UniProt
Find proteins for A0A2S9PFE9 (Yersinia pestis) Explore A0A2S9PFE9  Go to UniProtKB:  A0A2S9PFE9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	J [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE	E [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	G [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.198 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M34PV4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.299	α = 90
b = 82.865	β = 90
c = 110.091	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Osipiuk, J., Maltseva, N., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations