5Y9R | pdb_00005y9r

Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66

PDB DOI: https://doi.org/10.2210/pdb5Y9R/pdb

Classification: VIRAL PROTEIN
Organism(s): Bovine rotavirus G10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-28 Released: 2018-09-05
Deposition Author(s): Suguna, K., Kumar, S.
Funding Organization(s): Department of Biotechnology (DBT)-Indian Institute of Science, Partnership program for advanced Research in Biological Science and Bioengineering

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.238 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

New tetrameric forms of the rotavirus NSP4 with antiparallel helices

Suguna, K., Kumar, S.

To be published.

Macromolecule Content

Total Structure Weight: 23.08 kDa
Atom Count: 1,345
Modeled Residue Count: 169
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonstructural protein 4	A, B, C [auth D], D [auth C]	46	Bovine rotavirus G10	Mutation(s): 0
UniProt
Find proteins for Q6QT01 (Bovine rotavirus G10) Explore Q6QT01 Go to UniProtKB: Q6QT01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6QT01
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.238 (Depositor), 0.250 (DCC)
R-Value Work: 0.202 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.12	α = 90
b = 57.43	β = 90
c = 62.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Suguna, K.

Kumar, S.

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT)-Indian Institute of Science, Partnership program for advanced Research in Biological Science and Bioengineering	India	--