6EYT

Crystal structure of the Salmonella effector SseK3 in complex with UDP-GlcNAc and Manganese

PDB DOI: https://doi.org/10.2210/pdb6EYT/pdb

Classification: TOXIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-11-13 Released: 2018-02-28
Deposition Author(s): Esposito, D., Rittinger, K.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.241
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 75.51 kDa
Atom Count: 5,311
Modelled Residue Count: 618
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III secretion system effector protein	A, B	327	Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344	Mutation(s): 0 Gene Names: sseK3, SL1344_1928
UniProt
Find proteins for A0A0H3NMP8 (Salmonella typhimurium (strain SL1344)) Explore A0A0H3NMP8 Go to UniProtKB: A0A0H3NMP8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3NMP8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B]	F [auth A], K [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
NDG Query on NDG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A]	E [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.241
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.97	α = 90
b = 85.94	β = 90
c = 96.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Esposito, D.

Rittinger, K.

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001142

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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6EYT

Crystal structure of the Salmonella effector SseK3 in complex with UDP-GlcNAc and Manganese

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)