3TSL | pdb_00003tsl

Crystal structure of M-PMV DUTPASE relaxed end-product (dUMP) complex

PDB DOI: https://doi.org/10.2210/pdb3TSL/pdb

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

Deposited: 2011-09-13 Released: 2011-10-12
Deposition Author(s): Nemeth, V., Barabas, O., Vertessy, G.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.229 (Depositor), 0.232 (DCC)
R-Value Work:
0.193 (Depositor), 0.197 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 16.46 kDa
Atom Count: 870
Modeled Residue Count: 113
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.229 (Depositor), 0.232 (DCC)
R-Value Work: 0.193 (Depositor), 0.197 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.833	α = 90
b = 60.833	β = 90
c = 64.043	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.