7O2N | pdb_00007o2n

Crystal structure of B. subtilis UGPase YngB

• PDB DOI: https://doi.org/10.2210/pdb7O2N/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-30 Released: 2021-04-14 
• Deposition Author(s): Wu, C.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Characterisation of the Bacillus subtilis Uridylyltransferase YngB

Wu, C.

(2021) Ph D Thesis 

• DOI: https://doi.org/10.25560/91986

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: 66.12 kDa 
• Atom Count: 4,383 
• Modeled Residue Count: 580 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable UTP--glucose-1-phosphate uridylyltransferase YngB	A, B	296	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: yngB, BSU18180 EC: 2.7.7.9
UniProt
Find proteins for O31822 (Bacillus subtilis (strain 168)) Explore O31822  Go to UniProtKB:  O31822

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.156	α = 90
b = 158.979	β = 90
c = 180.317	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Wu, C.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2021-10-27
  Changes: Data collection, Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description