6PYM | pdb_00006pym

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.165 (Depositor), 0.195 (DCC)
R-Value Work:
0.159 (Depositor)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0Q2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.165 (Depositor), 0.195 (DCC)
R-Value Work: 0.159 (Depositor)
R-Value Observed: 0.159 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Narayana, S.V.L.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.