7N8V | pdb_00007n8v

Crystal structure of free ERI2 nuclease

• PDB DOI: https://doi.org/10.2210/pdb7N8V/pdb

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


• Deposited: 2021-06-15 Released: 2022-07-06 
• Deposition Author(s): Thapar, R., Arvai, A.S., Tainer, J.A.
• Funding Organization(s): Robert A. Welch Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI), Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of free ERI2 nuclease

Thapar, R., Arvai, A.S., Tainer, J.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.29 kDa 
• Atom Count: 3,489 
• Modeled Residue Count: 427 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERI1 exoribonuclease 2	A, B	264	Homo sapiens	Mutation(s): 0  Gene Names: ERI2, EXOD1, KIAA1504 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for A8K979 (Homo sapiens) Explore A8K979  Go to UniProtKB:  A8K979
PHAROS:  A8K979 GTEx:  ENSG00000196678

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.134	α = 90
b = 55.875	β = 105.029
c = 75.751	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Thapar, R., Arvai, A.S., Tainer, J.A.

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Funding Organization	Location	Grant Number
Robert A. Welch Foundation		--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA220430
Other private	United States	GAP Award (to R.T., J.A.T)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM076660-04S1
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description