3U8U | pdb_00003u8u

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

• PDB DOI: https://doi.org/10.2210/pdb3U8U/pdb

• Classification: HYDROLASE, LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-17 Released: 2011-10-26 
• Deposition Author(s): Agarwal, R., Naidu, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

Agarwal, R., Naidu, M.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 213.93 kDa 
• Atom Count: 13,631 
• Modeled Residue Count: 1,640 
• Deposited Residue Count: 1,908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) lyase	A, B, C, D, E, F	318	Homo sapiens	Mutation(s): 0  Gene Names: APEX1, APE, APE1, APEX, APX, HAP1, REF1 EC: 3.1 (PDB Primary Data), 4.2.99.18 (PDB Primary Data), 3.1.21 (UniProt), 3.1.11.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27695 (Homo sapiens) Explore P27695  Go to UniProtKB:  P27695
PHAROS:  P27695 GTEx:  ENSG00000100823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	H [auth A], J [auth B], L [auth C], P [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], I [auth B], K [auth C], M [auth D], N [auth E], O [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.84	α = 90
b = 97.284	β = 90.91
c = 132.15	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-26 
Deposition Author(s): Agarwal, R., Naidu, M.D.

Revision History  

• Version 1.0: 2011-10-26
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description