6YV5

Crystal Structure of Serine protease SplB N3Q/S154R from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb6YV5/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-04-27 Released: 2021-05-12
Deposition Author(s): Rangel Pereira, M.R., Brear, P., Knyphausen, P., Jermutus, L., Hollfelder, F.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.200
R-Value Work: 0.186
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Serine protease SplB N3Q/S154R from Staphylococcus aureus

Knyphausen, P., Rangel Pereira, M.R., Brear, P., Jermutus, L., Hollfelder, F.

To be published.

Macromolecule Content

Total Structure Weight: 22.65 kDa
Atom Count: 1,901
Modelled Residue Count: 206
Deposited Residue Count: 206
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease	A	206	Staphylococcus aureus	Mutation(s): 2 Gene Names: splB EC: 3.4.21
UniProt
Find proteins for Q2FXC3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXC3 Go to UniProtKB: Q2FXC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.200
R-Value Work: 0.186
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.92	α = 90
b = 64.34	β = 90
c = 73.15	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Rangel Pereira, M.R.

Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	695669

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2022-11-30
Changes: Database references, Structure summary
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.