2XRI

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
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 25.9 kDa
Atom Count: 1,776
Modelled Residue Count: 206
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43414
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.210
R-Value Work: 0.175
R-Value Observed: 0.177
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

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Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Revision History (Full details and data files)

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

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2XRI

Crystal structure of human ERI1 exoribonuclease 3

Crystal Structure of Human Eri1 Exoribonuclease 3

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)