6Z4U | pdb_00006z4u

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.257 (Depositor), 0.254 (DCC)
R-Value Work:
0.217 (Depositor)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
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
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.257 (Depositor), 0.254 (DCC)
R-Value Work: 0.217 (Depositor)
R-Value Observed: 0.219 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Revision History (Full details and data files)

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

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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.