6DQ3

Streptococcus pyogenes deacetylase PplD in complex with acetate

PDB DOI: https://doi.org/10.2210/pdb6DQ3/pdb

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

Deposited: 2018-06-10 Released: 2019-05-01
Deposition Author(s): Li, 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.216
R-Value Work: 0.180
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

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

Literature

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

Rush, J.S., Parajuli, P., Ruda, A., Li, J., Pohane, A.A., Zamakhaeva, S., Rahman, M.M., Chang, J.C., Gogos, A., Kenner, C.W., Lambeau, G., Federle, M.J., Korotkov, K.V., Widmalm, G., Korotkova, N.

(2022) Nat Commun 13: 590

DOI: https://doi.org/10.1038/s41467-022-28257-0

Macromolecule Content

Total Structure Weight: 52.7 kDa
Atom Count: 3,930
Modelled Residue Count: 453
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polysaccharide deacetylase	A, B	230	Streptococcus pyogenes	Mutation(s): 0 Gene Names: M5005_Spy0818
UniProt
Find proteins for J7M3C9 (Streptococcus pyogenes M1 476) Explore J7M3C9 Go to UniProtKB: J7M3C9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J7M3C9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B]	Q [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A] E [auth A] F [auth A] I [auth A] K [auth B] D [auth A], E [auth A], F [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	C [auth A], G [auth A], J [auth B], O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.216
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.16	α = 90
b = 78.43	β = 90
c = 138.07	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-01

Deposition Author(s):

Li, J.

Korotkova, N.

Korotkov, K.V.

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 (Full details and data files)

Version 1.0: 2019-05-01
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2022-02-09
Changes: Database references, Derived calculations, Structure summary

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Help and Resources

6DQ3

Streptococcus pyogenes deacetylase PplD in complex with acetate

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)