6MAO | pdb_00006mao

Crystal structure of Deoxyuridine 5'-triphosphate nucleotidohydrolase from Legionella pneumophila Philadelphia 1 in complex with dUMP (Deoxyuridine 5'-monophosphate)

• PDB DOI: https://doi.org/10.2210/pdb6MAO/pdb

• Classification: HYDROLASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-08-28 Released: 2018-09-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of dUTPase from Legionella pneumophila

Nguyen, C.L., Tramell, A.R., Norman, J.O., Abendroth, J., Barrett, K.F., Craig, J.K., Edwards, T.E., Lorimer, D.D., McLaughlin, K.J.

(2025) Acta Crystallogr F Struct Biol Commun 81: 155-162

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.91 kDa 
• Atom Count: 1,240 
• Modeled Residue Count: 137 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	160	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: dut, lpg2487 EC: 3.6.1.23
UniProt
Find proteins for Q5ZSN0 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSN0  Go to UniProtKB:  Q5ZSN0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	B [auth A]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36mao

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.67	α = 90
b = 85.67	β = 90
c = 55.46	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-04-09
  Changes: Database references, Structure summary