8HDA | pdb_00008hda

Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8HDA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-03 Released: 2022-12-21 
• Deposition Author(s): Ni, X.C., Lei, J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2

Ni, X.C., Lei, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.24 kDa 
• Atom Count: 1,619 
• Modeled Residue Count: 187 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	98	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.53	α = 90
b = 46.333	β = 90
c = 70.077	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Ni, X.C., Lei, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFF0702004

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description