2B0V | pdb_00002b0v

NUDIX hydrolase from Nitrosomonas europaea.

• PDB DOI: https://doi.org/10.2210/pdb2B0V/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-09-14 Released: 2005-09-27 
• Deposition Author(s): Osipiuk, J., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.206 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

X-ray structure of NUDIX hydrolase from Nitrosomonas europaea.

Osipiuk, J., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 17.56 kDa 
• Atom Count: 1,390 
• Modeled Residue Count: 148 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUDIX hydrolase	A	153	Nitrosomonas europaea	Mutation(s): 3  Gene Names: NE0184 EC: 3.6.1
UniProt
Find proteins for Q82XR9 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82XR9  Go to UniProtKB:  Q82XR9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.206 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.45	α = 90
b = 66.509	β = 90
c = 73.812	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Osipiuk, J., Skarina, T., Savchenko, A., Edwards, A., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary