2XRI | pdb_00002xri

Crystal structure of human ERI1 exoribonuclease 3

• PDB DOI: https://doi.org/10.2210/pdb2XRI/pdb

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


• Deposited: 2010-09-15 Released: 2010-09-29 
• Deposition Author(s): Welin, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Wahlberg, E., Weigelt, J., Nordlund, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Eri1 Exoribonuclease 3

Welin, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Wahlberg, E., Weigelt, J., Nordlund, P.

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: 25.9 kDa 
• Atom Count: 1,776 
• Modeled Residue Count: 206 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERI1 EXORIBONUCLEASE 3	A	224	Homo sapiens	Mutation(s): 0  EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43414 (Homo sapiens) Explore O43414  Go to UniProtKB:  O43414
PHAROS:  O43414 GTEx:  ENSG00000117419

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.72	α = 90
b = 76.9	β = 90
c = 86.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Welin, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Wahlberg, E., Weigelt, J., Nordlund, P.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Non-polymer description, Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description