6YV6 | pdb_00006yv6

Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb6YV6/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Staphylococcus aureus

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

To be published.

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: 23.23 kDa 
• Atom Count: 1,743 
• Modeled Residue Count: 200 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease	A	206	Staphylococcus aureus	Mutation(s): 3  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	B [auth A], C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.69	α = 90
b = 44.31	β = 92.94
c = 30.81	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Rangel Pereira, M.R., Brear, P., Knyphausen, P., Jermutus, L., Hollfelder, F.

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

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description