6YV5 | pdb_00006yv5

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 (Depositor), 0.200 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 206
Deposited Residue Count: 206
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.200 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (DCC)
R-Value Observed: 0.187 (Depositor)

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

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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

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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.