5UDM | pdb_00005udm

Phage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes, space group P6522

• PDB DOI: https://doi.org/10.2210/pdb5UDM/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes MGAS5005
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-27 Released: 2017-12-27 
• Deposition Author(s): Edgar, R.J., Korotkova, N., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Structure of phage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes

Edgar, R.J., Korotkova, N., Korotkov, K.V.

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.15 kDa 
• Atom Count: 3,418 
• Modeled Residue Count: 436 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage-associated cell wall hydrolase	A [auth B], B [auth A]	261	Streptococcus pyogenes MGAS5005	Mutation(s): 0  Gene Names: M5005_Spy1001

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B], D [auth B], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth B], B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.97	α = 90
b = 122.97	β = 90
c = 163.73	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Edgar, R.J., Korotkova, N., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R21AI113253
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Refinement description, Structure summary