8CGA

Structure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant

• PDB DOI: https://doi.org/10.2210/pdb8CGA/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-03 Released: 2024-05-15 
• Deposition Author(s): Toth, Z.S., Benedek, A., Leveles, I., Vertessy, B.G.
• Funding Organization(s): National Research Development and Innovation Office (NKFIH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.170 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Starting Model: experimental

Literature

Structure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant

Toth, Z.S., Benedek, A., Leveles, I., Vertessy, B.G.

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

Macromolecule Content

• Total Structure Weight: 18.39 kDa 
• Atom Count: 1,231 
• Modelled Residue Count: 142 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	169	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: dut, Rv2697c, MTCY05A6.18c EC: 3.6.1.23
UniProt
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNS5  Go to UniProtKB:  P9WNS5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP (Subject of Investigation/LOI)	B [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
TRS	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.170 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.249	α = 90
b = 55.249	β = 90
c = 83.751	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Toth, Z.S., Benedek, A., Leveles, I., Vertessy, B.G.

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Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	Hungary	K119493
National Research Development and Innovation Office (NKFIH)	Hungary	K135231
National Research Development and Innovation Office (NKFIH)	Hungary	VEKOP-2.3.2-16-2017-00013
National Research Development and Innovation Office (NKFIH)	Hungary	NKP-2018-1.2.1-NKP-2018-00005
National Research Development and Innovation Office (NKFIH)	Hungary	TKP2021-EGA-02

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release