8D34

Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A

PDB DOI: https://doi.org/10.2210/pdb8D34/pdb

Classification: RNA BINDING PROTEIN,VIRAL PROTEIN,LYASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-05-31 Released: 2023-06-14
Deposition Author(s): Farraj, R.A., Edwards, R.A., Glover, J.N.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.263
R-Value Work: 0.246
R-Value Observed: 0.247

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A

Farraj, R.A., Edwards, R.A., Glover, J.N.M.

To be published.

Macromolecule Content

Total Structure Weight: 83.64 kDa
Atom Count: 5,488
Modelled Residue Count: 696
Deposited Residue Count: 746
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease nsp15	A, B	373	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: rep, 1a-1b EC: 4.6.1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.263
R-Value Work: 0.246
R-Value Observed: 0.247
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.525	α = 90
b = 152.525	β = 90
c = 109.644	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.