8P6K | pdb_00008p6k

Structure of the hypervariable region of Streptococcus pyogenes M3 protein

PDB DOI: https://doi.org/10.2210/pdb8P6K/pdb

Classification: PROTEIN BINDING
Organism(s): Streptococcus pyogenes serotype M3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-05-26 Released: 2023-07-05
Deposition Author(s): Wojnowska, M., Schwarz-Linek, U.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.268 (Depositor), 0.267 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structural basis for collagen recognition by the Streptococcus pyogenes M3 protein and its involvement in biofilm

Wojnowska, M., Wajima, T., Yelland, T., Ludewig, H., Hagan, R.M., Watt, G., Hamaia, S.W., Bihan, D., Malcor, J.D., Bonna, A., Bergsten, H., Svensson, M., Oppegaard, O., Skrede, S., Arnell, P., Hyldegaard, O., Farndale, R.W., Norrby-Teglund, A., Schwarz-Linek, U.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.12.17.628954

Macromolecule Content

Total Structure Weight: 26.55 kDa
Atom Count: 1,868
Modeled Residue Count: 218
Deposited Residue Count: 226
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiphagocytic M protein, type 3	A [auth BBB], B [auth CCC]	113	Streptococcus pyogenes serotype M3	Mutation(s): 1 Gene Names: emm3, SpyM3_1727
UniProt
Find proteins for A0A0H2UWN1 (Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)) Explore A0A0H2UWN1 Go to UniProtKB: A0A0H2UWN1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UWN1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.268 (Depositor), 0.267 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.474	α = 90
b = 24.107	β = 105.287
c = 78.007	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Schwarz-Linek, U.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009681/1

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Structure summary
Version 1.2: 2025-01-15
Changes: Database references

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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.