8RSJ

Crystal structure of Methanobrevibacter oralis macrodomain in complex with ADPr in open conformation

• PDB DOI: https://doi.org/10.2210/pdb8RSJ/pdb

• Classification: HYDROLASE
• Organism(s): Methanobrevibacter oralis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-24 Released: 2024-09-25 
• Deposition Author(s): Ariza, A.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.232 
• R-Value Work: 0.192 

Starting Model: experimental

Literature

Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains

Ariza, A., Liu, Q., Cowleson, N., Ahel, I., Filippov, D.V., Rack, J.G.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.69 kDa 
• Atom Count: 5,164 
• Modelled Residue Count: 523 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-acetyl-ADP-ribose deacetylase	A, B	262	Methanobrevibacter oralis	Mutation(s): 0  Gene Names: ymdB, MBORA_13990 EC: 3.5.1
UniProt
Find proteins for A0A166ACJ5 (Methanobrevibacter oralis) Explore A0A166ACJ5  Go to UniProtKB:  A0A166ACJ5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JNT (Subject of Investigation/LOI)	D [auth A], F [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate C15 H25 N5 O14 P2 QKJRZYRQRSLXSV-AOOZFPJJSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.232 
• R-Value Work: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.986	α = 90
b = 58.101	β = 117.664
c = 76.269	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Ariza, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	210634
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R007195/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W016613/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/X007472/1

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release