6KNJ | pdb_00006knj

UTP-bound UGPase from acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6KNJ/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-05 Released: 2020-08-12 
• Deposition Author(s): Lee, J.H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

UTP-bound UGPase from acinetobacter baumannii

Kang, L.W.

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)

Macromolecule Content 

• Total Structure Weight: 64.52 kDa 
• Atom Count: 4,301 
• Modeled Residue Count: 570 
• Deposited Residue Count: 580 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A	290	Acinetobacter baumannii	Mutation(s): 0  Gene Names: galU, B9X91_19205, CBI29_00108, CSB70_3798, DVA79_14980 EC: 2.7.7.9
UniProt
Find proteins for X2KZJ9 (Acinetobacter baumannii) Explore X2KZJ9  Go to UniProtKB:  X2KZJ9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	B	290	Acinetobacter baumannii	Mutation(s): 0  Gene Names: galU, B9X91_19205, CBI29_00108, CSB70_3798, DVA79_14980 EC: 2.7.7.9
UniProt
Find proteins for X2KZJ9 (Acinetobacter baumannii) Explore X2KZJ9  Go to UniProtKB:  X2KZJ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP (Subject of Investigation/LOI)	D [auth A], E [auth B]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.376	α = 90
b = 117.376	β = 90
c = 110.275	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Lee, J.H., Kang, L.W.

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description