6MJK | pdb_00006mjk

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine

• PDB DOI: https://doi.org/10.2210/pdb6MJK/pdb

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


• Deposited: 2018-09-21 Released: 2018-10-31 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine

Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.3 kDa 
• Atom Count: 1,343 
• Modeled Residue Count: 144 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dUTP pyrophosphatase	A	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUR	D [auth A]	2'-DEOXYURIDINE C9 H12 N2 O5 MXHRCPNRJAMMIM-SHYZEUOFSA-N
PPV	E [auth A]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.23	α = 90
b = 74.23	β = 90
c = 74.23	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description