5IYN | pdb_00005iyn

Protruding domain of GII.4 human norovirus CHDC2094

PDB DOI: https://doi.org/10.2210/pdb5IYN/pdb

Classification: VIRAL PROTEIN
Organism(s): Norovirus Hu/GII.4/CHDC2094/1974/US
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-24 Released: 2017-04-05
Deposition Author(s): Singh, B.K., Hansman, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.175 (Depositor), 0.178 (DCC)
R-Value Work:
0.152 (Depositor), 0.155 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5IYN

This is version 2.0 of the entry. See complete history.

Literature

Four decades of structural evolution of GII.4 norovirus

Singh, B.K., Hansman, G.S.

To be published.

Macromolecule Content

Total Structure Weight: 68.04 kDa
Atom Count: 5,385
Modeled Residue Count: 609
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	306	Norovirus Hu/GII.4/CHDC2094/1974/US	Mutation(s): 0
UniProt
Find proteins for D0QJ68 (Norovirus Hu/GII.4/CHDC2094/1974/US) Explore D0QJ68 Go to UniProtKB: D0QJ68
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0QJ68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.175 (Depositor), 0.178 (DCC)
R-Value Work: 0.152 (Depositor), 0.155 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.19	α = 90
b = 105.92	β = 90
c = 135.86	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 2.0: 2024-05-08
Changes: Atomic model, Data collection, Database references

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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.