6PYM

Structure of active-site serine mutant of ESP, serine protease from Staphylococcus epidermidis

• PDB DOI: https://doi.org/10.2210/pdb6PYM/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-30 Released: 2019-08-14 
• Deposition Author(s): Manne, K., Narayana, S.V.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.165 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Literature

Structural insights into the role of the N-terminus in the activation and function of extracellular serine protease from Staphylococcus epidermidis

Manne, K., Narayana, S.V.L.

(2020) Acta Crystallogr D Biol Crystallogr 76: 28-40

• DOI: https://doi.org/10.1107/S2059798319015055

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 23.59 kDa 
• Atom Count: 1,945 
• Modelled Residue Count: 213 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl endopeptidase	A	216	Staphylococcus epidermidis ATCC 12228	Mutation(s): 1  Gene Names: gseA, esp, SE_1543 EC: 3.4.21.19
UniProt
Find proteins for P0C0Q2 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore P0C0Q2  Go to UniProtKB:  P0C0Q2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.165 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.621	α = 90
b = 61.026	β = 98.66
c = 42.512	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Manne, K., Narayana, S.V.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01- AI106808

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2020-01-08
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description