6S5I | pdb_00006s5i

Structure of the Lausanne variant of myxoma virus M062 protein

PDB DOI: https://doi.org/10.2210/pdb6S5I/pdb

Classification: VIRAL PROTEIN
Organism(s): Myxoma virus
Expression System: Escherichia coli str. 'clone D i2
Mutation(s): Yes

Deposited: 2019-07-01 Released: 2021-12-01
Deposition Author(s): O'Byrne, P., Khan, A.R.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.266 (Depositor), 0.270 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Lausanne variant of myxoma virus M062 protein

O'Byrne, P., Khan, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 18.71 kDa
Atom Count: 1,271
Modeled Residue Count: 156
Deposited Residue Count: 161
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M62R	A	161	Myxoma virus	Mutation(s): 3 Gene Names: m062R, MYXV_gp066
UniProt
Find proteins for P68550 (Myxoma virus (strain Lausanne)) Explore P68550 Go to UniProtKB: P68550
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68550
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.266 (Depositor), 0.270 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.827	α = 90
b = 94.827	β = 90
c = 44.136	γ = 120

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	SFI 12/1A/1239

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Refinement description

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.