Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 37.42 kDa 
• Atom Count: 2419 
• Residue Count: 286 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

7CD6

mAPE1-recessed dsDNA product complex

• DOI: 10.2210/pdb7CD6/pdb
• NDB: 7CD6

• Classification: HYDROLASE/DNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-18 Released: 2021-01-13 
• Deposition Author(s): Liu, T.C., Hsiao, Y.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.220 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 

Literature

APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling

Liu, T.C., Hsiao, Y.Y.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) endonuclease	A	308	Mus musculus	Mutation(s): 0  Gene Names: Apex1, Ape, Apex, Ref1 EC: 3.1
Find proteins for P28352 (Mus musculus) Explore P28352  Go to UniProtKB:  P28352

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3')	B	9	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.220 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.65	α = 90
b = 124.65	β = 90
c = 138.467	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-18 
• Released Date: 2021-01-13 
Deposition Author(s): Liu, T.C., Hsiao, Y.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST 109-2636-B-009-004

Revision History 

• Version 1.0: 2021-01-13
  Type: Initial release