5ROB | pdb_00005rob

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 helicase

PDB DOI: https://doi.org/10.2210/pdb5ROB/pdb
Deposition Group: G_1002166 (ground state) | Explore G_1002166

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

Deposited: 2020-09-22 Released: 2021-03-10
Deposition Author(s): Newman, J.A., Yosaatmadja, Y., Douangamath, A., Aimon, A., Powell, A.J., Dias, A., Fearon, D., Dunnett, L., Brandao-Neto, J., Krojer, T., Skyner, R., Gorrie-Stone, T., Thompson, W., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.219 (Depositor), 0.225 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5ROB

This is version 1.2 of the entry. See complete history.

Literature

PanDDA analysis group deposition of ground-state model

Newman, J.A., Yosaatmadja, Y., Douangamath, A., Aimon, A., Powell, A.J., Dias, A., Fearon, D., Dunnett, L., Brandao-Neto, J., Krojer, T., Skyner, R., Gorrie-Stone, T., Thompson, W., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 134.63 kDa
Atom Count: 9,407
Modeled Residue Count: 1,157
Deposited Residue Count: 1,202
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase	A [auth B], B [auth A]	601	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	F [auth B], G [auth B], K [auth A], L [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain K [auth A] Focus chain L [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth B] D [auth B] E [auth B] H [auth A] I [auth A] C [auth B], D [auth B], E [auth B], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.254 (Depositor), 0.258 (DCC)
R-Value Work: 0.219 (Depositor), 0.225 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.242	α = 102.4
b = 70.282	β = 95.71
c = 84.616	γ = 112.84

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-03-10

Deposition Author(s):

Yosaatmadja, Y.

Douangamath, A.

Brandao-Neto, J.

Gorrie-Stone, T.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2021-03-10
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2026-02-18
Changes: Refinement description, Structure summary

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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.