7BPD | pdb_00007bpd

Crystal structural analysis of Swine dUTPase

• PDB DOI: https://doi.org/10.2210/pdb7BPD/pdb

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


• Deposited: 2020-03-22 Released: 2021-03-24 
• Deposition Author(s): Liang, R., Peng, G.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structural analysis of swine dUTPase

Liang, R., Peng, G.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.07 kDa 
• Atom Count: 2,273 
• Modeled Residue Count: 264 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine triphosphatase	A, B	169	Sus scrofa	Mutation(s): 0  Gene Names: DUT EC: 3.6.1.23
UniProt
Find proteins for A0A480PG39 (Sus scrofa) Explore A0A480PG39  Go to UniProtKB:  A0A480PG39

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.175	α = 90
b = 54.535	β = 116.68
c = 52.107	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Liang, R., Peng, G.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31722056

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary