5VJY | pdb_00005vjy

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri

• PDB DOI: https://doi.org/10.2210/pdb5VJY/pdb

• Classification: HYDROLASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-20 Released: 2017-05-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri

Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

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 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.32 kDa 
• Atom Count: 5,696 
• Modeled Residue Count: 658 
• Deposited Residue Count: 775 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dUTP pyrophosphatase	A, B, C, D, E	155	Naegleria fowleri	Mutation(s): 0  EC: 3.6.1.23
UniProt
Find proteins for A0A1Z0YU86 (Naegleria fowleri) Explore A0A1Z0YU86  Go to UniProtKB:  A0A1Z0YU86

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	F [auth A], H [auth B], I [auth C], J [auth D], K [auth E]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.64	α = 90
b = 118.64	β = 90
c = 98.98	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description