[English] 日本語
Yorodumi
- PDB-2xkm: Consensus structure of Pf1 filamentous bacteriophage from X-ray f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xkm
TitleConsensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR
ComponentsCAPSID PROTEIN G8P
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / TRANSMEMBRANE / VIRION / VIRUS COAT PROTEIN
Function / homology
Function and homology information


helical viral capsid / host cell membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #230 / Inovirus Coat protein B / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS PHAGE PF1 (virus)
MethodFIBER DIFFRACTION / SOLID-STATE NMR / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsStraus, S.K. / P Scott, W.R. / Schwieters, C.D. / Marvin, D.A.
Citation
Journal: Eur.Biophys.J. / Year: 2011
Title: Consensus Structure of Pf1 Filamentous Bacteriophage from X-Ray Fibre Diffraction and Solid-State NMR.
Authors: Straus, S.K. / Scott, W.R. / Schwieters, C.D. / Marvin, D.A.
#1: Journal: Protein Sci. / Year: 2005
Title: Structural Basis of the Temperature Transition of Pf1 Bacteriophage.
Authors: Thiriot, D.S. / Nevzorov, A.A. / Opella, S.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Pf1 Filamentous Bacteriophage: Refinement of a Molecular Model by Simulated Annealing Using 3.3 A Resolution X-Ray Fibre Diffraction Data.
Authors: Gonzalez, A. / Nave, C. / Marvin, D.A.
#3: Journal: Eur.Biophys.J. / Year: 2008
Title: The Hand of the Filamentous Bacteriophage Helix.
Authors: Straus, S.K. / Scott, W.R.P. / Marvin, D.A.
#4: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions.
Authors: Marvin, D.A.
History
DepositionJul 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Data collection / Database references ...Data collection / Database references / Other / Version format compliance
Revision 1.2Sep 18, 2019Group: Data collection / Category: reflns
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.percent_possible_obs
Revision 1.3Apr 28, 2021Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_sf / _reflns.pdbx_redundancy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CAPSID PROTEIN G8P


Theoretical massNumber of molelcules
Total (without water)4,6121
Polymers4,6121
Non-polymers00
Water0
1
A: CAPSID PROTEIN G8P
x 35


Theoretical massNumber of molelcules
Total (without water)161,43435
Polymers161,43435
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation34
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative
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 °)
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = 65.915 DEGREES RISE PER SUBUNIT (HEIGHT) = 3.05 ANGSTROMS COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A CYLINDRICAL SHELL SURROUNDING A DNA CORE.

-
Components

#1: Protein/peptide CAPSID PROTEIN G8P / / MAJOR COAT PROTEIN / GENE 8 PROTEIN / G8P / COAT PROTEIN B / PF1 PHAGE COAT PROTEIN GENE 8


Mass: 4612.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-82 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS PHAGE PF1 (virus) / References: UniProt: P03621

-
Experimental details

-
Experiment

Experiment
Method
FIBER DIFFRACTION
SOLID-STATE NMR

-
Sample preparation

CrystalDescription: NONE

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→12 Å / Num. obs: 3548 / Observed criterion σ(I): 0.8

-
Processing

SoftwareName: XPLOR-NIH / Classification: phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IFM

4ifm


Highest resolution: 3.3 Å
Refinement stepCycle: LAST / Highest resolution: 3.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms322 0 0 0 322
NMR ensembleConformers submitted total number: 1

+
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