5JD8

Crystal structure of the serine endoprotease from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb5JD8/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-15 Released: 2016-05-04 
• Deposition Author(s): Filippova, E.V., Wawrzsak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.183 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Starting Model: experimental

Literature

Crystal structure of the serine endoprotease from Yersinia pestis

Filippova, E.V., Wawrzsak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 35.78 kDa 
• Atom Count: 2,218 
• Modelled Residue Count: 272 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic serine peptidase DegS	A	334	Yersinia pestis CO92	Mutation(s): 0  Gene Names: degS, AK38_3169 EC: 3.4.21
UniProt
Find proteins for A0A5P8YL96 (Yersinia pestis) Explore A0A5P8YL96  Go to UniProtKB:  A0A5P8YL96

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	B [auth A]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.183 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: H 3
• Diffraction Data: https://doi.org/10.18430/m35jd8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.418	α = 90
b = 104.418	β = 90
c = 76.015	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Filippova, E.V., Wawrzsak, Z., Sandoval, J., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description