5VE7 | pdb_00005ve7

Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP

• PDB DOI: https://doi.org/10.2210/pdb5VE7/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-04 Released: 2017-04-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP

Abendroth, J., Higgins, T.W., Dranow, D.M., 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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.78 kDa 
• Atom Count: 2,384 
• Modeled Residue Count: 282 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A	302	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_1359 EC: 2.7.7.9
UniProt
Find proteins for B1YNX3 (Burkholderia ambifaria (strain MC40-6)) Explore B1YNX3  Go to UniProtKB:  B1YNX3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP	B [auth A]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VE7

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.25	α = 90
b = 108.48	β = 90
c = 124.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Advisory
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description