Biological Assembly 1  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 60592.68 
• Atom Count: 3721 
• Residue Count: 535 
• Unique protein chains: 2

6B7M

Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin

• DOI: 10.2210/pdb6B7M/pdb

• Classification: CELL INVASION
• Organism(s): Homo sapiens, Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2017-10-04 Released: 2018-04-18 
• Deposition Author(s): Mao, Y., Akturk, A., Wasilko, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 

Literature

Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector.

Akturk, A., Wasilko, D.J., Wu, X., Liu, Y., Zhang, Y., Qiu, J., Luo, Z.Q., Reiter, K.H., Brzovic, P.S., Klevit, R.E., Mao, Y.

(2018) Nature 557: 729-733

• PubMed: 29795346 
• Primary Citation of Related Structures:  
  6B7Q, 6B7P, 6B7O

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SdeD (lpg2509)	A	383	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)	Mutation(s): 0
Find proteins for Q5ZSK8 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Go to UniProtKB:  Q5ZSK8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-C	B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB:  P0CG48

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 64.765	α = 90.00
b = 58.593	β = 114.66
c = 74.124	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
AMoRE	phasing
HKL-2000	data reduction
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-04 
• Released Date: 2018-04-18 
• Deposition Author(s): Mao, Y., Akturk, A., Wasilko, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	R01-GM094347

Revision History 

• Version 1.0: 2018-04-18
  Type: Initial release
• Version 1.1: 2018-06-06
  Type: Data collection, Database references
• Version 1.2: 2018-06-13
  Type: Data collection, Database references
• Version 1.3: 2019-02-20
  Type: Author supporting evidence, Data collection