9YFB | pdb_00009yfb

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with UTP

• PDB DOI: https://doi.org/10.2210/pdb9YFB/pdb

• Classification: TRANSFERASE
• Organism(s): Bordetella pertussis Tohama I
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-25 Released: 2025-10-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis in complex with UTP

Seibold, S., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.52 kDa 
• Atom Count: 2,222 
• Modeled Residue Count: 272 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A	285	Bordetella pertussis Tohama I	Mutation(s): 0  Gene Names: BP3403 EC: 2.7.7.9
UniProt
Find proteins for Q7VTV0 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTV0  Go to UniProtKB:  Q7VTV0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP (Subject of Investigation/LOI)	D [auth A]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N
MG (Subject of Investigation/LOI)	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39YFB

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.672	α = 90
b = 73.672	β = 90
c = 118.422	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release