8DMS

Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose

• PDB DOI: https://doi.org/10.2210/pdb8DMS/pdb

• Classification: ANTITOXIN
• Organism(s): Legionella pneumophila, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-08 Released: 2023-07-12 
• Deposition Author(s): Zhang, Z., Das, C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.207 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose

Zhang, Z., Das, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 106.62 kDa 
• Atom Count: 7,558 
• Modelled Residue Count: 888 
• Deposited Residue Count: 948 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MavL	A, B	399	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for Q5ZSJ1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSJ1  Go to UniProtKB:  Q5ZSJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, D	75	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	E [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
1PE	F [auth C]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
FLC	I [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GVE	G [auth C], H [auth D]	METHYL 4-AMINOBUTANOATE C5 H11 N O2 KVQGGLZHHFGHPU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.207 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.957	α = 90
b = 108.957	β = 90
c = 209.546	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Zhang, Z., Das, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01GM126296
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI148103

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations