7N6S

Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)

• PDB DOI: https://doi.org/10.2210/pdb7N6S/pdb

• Classification: HYDROLASE
• Organism(s): Rickettsia prowazekii str. Madrid E
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-09 Released: 2021-06-23 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)

Abendroth, J., deBouver, N.D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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 Evidence: gel filtration

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)

Macromolecule Content

• Total Structure Weight: 100.15 kDa 
• Atom Count: 7,233 
• Modelled Residue Count: 860 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C, D, E, F	152	Rickettsia prowazekii str. Madrid E	Mutation(s): 0  Gene Names: dut, RP399 EC: 3.6.1.23
UniProt
Find proteins for Q9ZDD2 (Rickettsia prowazekii (strain Madrid E)) Explore Q9ZDD2  Go to UniProtKB:  Q9ZDD2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m37n6s

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.72	α = 90
b = 87	β = 90
c = 183.34	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description