6Z4U

X-ray Crystallographic Structure of Orf9b from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb6Z4U/pdb

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


• Deposited: 2020-05-25 Released: 2020-06-17 
• Deposition Author(s): Weeks, S.D., De Graef, S., Munawar, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

X-ray Crystallographic Structure of Orf9b from SARS-CoV-2

Weeks, S.D., De Graef, S., Munawar, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.15 kDa 
• Atom Count: 1,312 
• Modelled Residue Count: 166 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein 9b	A, B	97	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTD2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD2  Go to UniProtKB:  P0DTD2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	C [auth B]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.03	α = 90
b = 64.571	β = 90
c = 73.536	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Weeks, S.D., De Graef, S., Munawar, A.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description