7MXR | pdb_00007mxr

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (r-2)

• PDB DOI: https://doi.org/10.2210/pdb7MXR/pdb
• NAKB: 7MXR

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


• Deposited: 2021-05-19 Released: 2023-05-10 
• Deposition Author(s): Shi, Y., Beese, L.S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities

Shi, Y., Hellinga, H.W., Beese, L.S.

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)

Macromolecule Content 

• Total Structure Weight: 47.54 kDa 
• Atom Count: 3,242 
• Modeled Residue Count: 370 
• Deposited Residue Count: 381 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exonuclease 1	A [auth Z]	358	Homo sapiens	Mutation(s): 0  Gene Names: EXO1, EXOI, HEX1 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ84 (Homo sapiens) Explore Q9UQ84  Go to UniProtKB:  Q9UQ84
PHAROS:  Q9UQ84 GTEx:  ENSG00000174371

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')	B [auth A]	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')	C [auth B]	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	D [auth Z], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	E [auth Z]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.15	α = 90
b = 74.15	β = 90
c = 180.737	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Shi, Y., Beese, L.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 GM091487
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description