9JAX | pdb_00009jax

Crystal structure of NUDIX hydrolase from Bacillus methanolicus

• PDB DOI: https://doi.org/10.2210/pdb9JAX/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus methanolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-25 Released: 2025-09-03 
• Deposition Author(s): Kong, X.D., Ma, B.D.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of NUDIX hydrolase from Bacillus methanolicus

Kong, X.D., Ma, B.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.62 kDa 
• Atom Count: 5,943 
• Modeled Residue Count: 705 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose pyrophosphatase	A [auth E], B [auth A], C [auth B], D [auth C]	191	Bacillus methanolicus	Mutation(s): 0  Gene Names: act, BMMGA3_11130 EC: 3.6.1.13
UniProt
Find proteins for I3EA59 (Bacillus methanolicus (strain MGA3 / ATCC 53907)) Explore I3EA59  Go to UniProtKB:  I3EA59

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4K	I [auth B]	polyethylene glycol C30 H62 O15 WWPGFZAAWXFBTF-UHFFFAOYSA-N
MES	G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	E, F [auth E], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.71	α = 90
b = 98.31	β = 110.41
c = 73.5	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Kong, X.D., Ma, B.D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFA0911000

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release