[English] 日本語
Yorodumi
- PDB-7u0v: Structure of myxoma virus M062 protein variant Lau -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u0v
TitleStructure of myxoma virus M062 protein variant Lau
ComponentsProbable host range protein 2-1
KeywordsVIRAL PROTEIN / myxoma virus / M062 / SAMD9 / C7L superfamily / host-range factor / innate immunity / viral antagonism
Function / homologyPoxvirus C7/F8A / Poxvirus C7/F8A protein / viral process / NICKEL (II) ION / Probable host range protein 2-1
Function and homology information
Biological speciesMyxoma virus Homo sapiens
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsO'Byrne, P. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation IrelandSFI 12/1A/1239 Ireland
CitationJournal: To Be Published
Title: Structure of myxoma virus M062 protein variant MAV
Authors: O'Byrne, P. / Khan, A.R.
History
DepositionFeb 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable host range protein 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7092
Polymers18,6501
Non-polymers591
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.827, 94.827, 44.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein Probable host range protein 2-1 / M062


Mass: 18650.213 Da / Num. of mol.: 1 / Mutation: C90S,C107S,C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxoma virus (strain Lausanne)Homo sapiens
Strain: Lausanne / Gene: m062R / Production host: Escherichia coli (E. coli) / References: UniProt: P68550
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 50mM MgCl2 14% ethylene glycol 6% PEG8K 0.1M Tris pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→82.123 Å / % possible obs: 99.55 % / Redundancy: 9.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05385 / Rpim(I) all: 0.0184 / Rrim(I) all: 0.057 / Net I/σ(I): 23.92
Reflection shellResolution: 2.45→2.528 Å / Num. unique obs: 846 / CC1/2: 0.407

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cyw

5cyw


Resolution: 2.45→47.41 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 36.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 873 10.31 %
Rwork0.2112 7596 -
obs0.2169 8469 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.63 Å2 / Biso mean: 96.5222 Å2 / Biso min: 56.08 Å2
Refinement stepCycle: final / Resolution: 2.45→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 1 0 1271
Biso mean--117.81 --
Num. residues----156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.60340.48751260.4621279100
2.6034-2.80440.41011540.3431242100
2.8044-3.08670.36211600.2621242100
3.0867-3.53330.33511380.23621267100
3.5333-4.45160.26581510.19841276100
4.4516-47.410.20381440.1771129098
Refinement TLS params.Method: refined / Origin x: 8.5101 Å / Origin y: 34.1145 Å / Origin z: 34.3344 Å
111213212223313233
T0.6544 Å20.0031 Å20.0806 Å2-0.8433 Å20.0165 Å2--0.6976 Å2
L4.4085 °2-0.0517 °22.4249 °2-3.8595 °21.4463 °2--3.6844 °2
S0.1364 Å °0.1045 Å °-0.2541 Å °0.0466 Å °-0.3291 Å °0.2793 Å °0.1278 Å °-0.4667 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 156
2X-RAY DIFFRACTION1allB1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more