4GCY | pdb_00004gcy

Structure of Mycobacterium tuberculosis dUTPase H21W mutant

• PDB DOI: https://doi.org/10.2210/pdb4GCY/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-07-31 Released: 2013-07-03 
• Deposition Author(s): Toth, J., Vertessy, B.G., Leveles, I., Bendes, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Literature

RAMD identification of substrate binding pathways to the active site of dUTPase

Toth, J., Vertessy, B.G., Leveles, I., Bendes, A., Lopata, A.

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)

Macromolecule Content 

• Total Structure Weight: 18.75 kDa 
• Atom Count: 1,411 
• Modeled Residue Count: 163 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	174	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: dut, Rv2697c, MT2771, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP	B [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.94	α = 90
b = 54.94	β = 90
c = 83.86	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Toth, J., Vertessy, B.G., Leveles, I., Bendes, A.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations