[English] 日本語
Yorodumi
- PDB-2ifo: MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOME... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ifo
TitleMODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOMETRIC THEME
ComponentsINOVIRUS
KeywordsVIRUS / Helical virus
Function / homologyInovirus Coat protein B / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesFilamentous phage (virus)
MethodFIBER DIFFRACTION
AuthorsMarvin, D.A.
Citation
Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-building studies of Inovirus: genetic variations on a geometric theme.
Authors: Marvin, D.A.
#1: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
Authors: Marvin, D.A.
#2: Journal: J.Mol.Biol. / Year: 1974
Title: Filamentous Bacterial Viruses Xii. Molecular Architecture of the Class II (Pf1, Xf) Virion
Authors: Marvin, D.A. / Wiseman, R.L. / Wachtel, E.J.
History
DepositionAug 8, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INOVIRUS


Theoretical massNumber of molelcules
Total (without water)4,4591
Polymers4,4591
Non-polymers00
Water00
1
A: INOVIRUS
x 35


Theoretical massNumber of molelcules
Total (without water)156,07435
Polymers156,07435
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation34
identity operation1_555x,y,z1
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 35 / Rise per n subunits: 3.05 Å / Rotation per n subunits: 65.915 °)

-
Components

#1: Protein/peptide INOVIRUS


Mass: 4459.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Filamentous phage (virus) / Strain: XF MAJOR / References: UniProt: P03622
Sequence detailsTHE SEQUENCE USED IS AN UNPUBLISHED SEQUENCE CITED BY DAY ET AL., ANN. REV. BIOPHYS. BIOPHYS. CHEM. ...THE SEQUENCE USED IS AN UNPUBLISHED SEQUENCE CITED BY DAY ET AL., ANN. REV. BIOPHYS. BIOPHYS. CHEM. V. 17, 509, 1988.

-
Experimental details

-
Experiment

ExperimentMethod: FIBER DIFFRACTION

-
Processing

SoftwareName: EREF / Classification: refinement
RefinementDetails: THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE ARBITRARY VALUE OF 10.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms312 0 0 0 312

+
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