3TPY

Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites

• PDB DOI: https://doi.org/10.2210/pdb3TPY/pdb

• Classification: HYDROLASE
• Organism(s): Mason-Pfizer monkey virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-09-08 Released: 2011-10-12 
• Deposition Author(s): Barabas, O., Nemeth, V., Vertessy, B.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion

Barabas, O., Nemeth, V., Bodor, A., Perczel, A., Rosta, E., Kele, Z., Zagyva, I., Szabadka, Z., Grolmusz, V.I., Wilmanns, M., 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)

Macromolecule Content

• Total Structure Weight: 17.08 kDa 
• Atom Count: 1,038 
• Modelled Residue Count: 113 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE	A	152	Mason-Pfizer monkey virus	Mutation(s): 1  Gene Names: gag-pro EC: 3.6.1.23
UniProt
Find proteins for P07570 (Mason-Pfizer monkey virus) Explore P07570  Go to UniProtKB:  P07570

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP	D [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
UMP	E [auth A]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.559	α = 90
b = 60.559	β = 90
c = 63.635	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Barabas, O., Nemeth, V., Vertessy, B.G.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description