9MZB | pdb_00009mzb

X-ray crystallographic structure of Orf9b Apo Homodimer

PDB DOI: https://doi.org/10.2210/pdb9MZB/pdb

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

Deposited: 2025-01-22 Released: 2025-02-26
Deposition Author(s): San Felipe, C.J., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.341 (Depositor), 0.338 (DCC)
R-Value Work:
0.286 (Depositor), 0.287 (DCC)
R-Value Observed:
0.291 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

X-ray Crystallographic Structure of Refolded Apo-Orf9b Homodimer

San Felipe, C.J., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 21.69 kDa
Atom Count: 1,174
Modeled Residue Count: 150
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF9b protein	A, B	97	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: 9b
UniProt
Find proteins for P0DTD2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD2 Go to UniProtKB: P0DTD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLY (Subject of Investigation/LOI) Query on GLY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.341 (Depositor), 0.338 (DCC)
R-Value Work: 0.286 (Depositor), 0.287 (DCC)
R-Value Observed: 0.291 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.28	α = 90
b = 75.28	β = 90
c = 80.21	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

San Felipe, C.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.