[English] 日本語
Yorodumi
- PDB-2bic: The solution structure of the recombinant elicitor protein PcF fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bic
TitleThe solution structure of the recombinant elicitor protein PcF from the oomycete pathogen P. cactorum
ComponentsPHYTOTOXIC PROTEIN PCF
KeywordsTOXIN / PLANT PATHOGEN / PHYTOPHTHORA CACTORUM FRAGARIA PROTEIN / OOMYCETE PLANT PATHOGEN / ELICITIN FAMILY
Function / homologyHelix Hairpins - #540 / Phytotoxin, PcF / Phytotoxin PcF protein / Helix Hairpins / Helix non-globular / Special / Phytotoxic protein PcF
Function and homology information
Biological speciesPHYTOPHTHORA CACTORUM (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsNicastro, G. / Orsomando, G. / Desario, F. / Ferrari, E. / Manconi, L. / Spisni, A. / Ruggieri, S.
Citation
Journal: Protein Sci. / Year: 2009
Title: Solution Structure of the Phytotoxic Protein Pcf: The First Characterized Member of the Phytophthora Pcf Toxin Family.
Authors: Nicastro, G. / Orsomando, G. / Ferrari, E. / Manconi, L. / Desario, F. / Amici, A. / Naso, A. / Carpaneto, A. / Pertinhez, T.A. / Ruggieri, S. / Spisni, A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Characterization, and Cdna Sequencing of a Novel Hydroproline-Containing Factor Secreted by the Strawberry Pathogen Phytophtora Cactorum
Authors: Orsomando, G. / Lorenzi, M. / Raffaelli, M. / Dalla Rizza, N. / Mezzetti, M. / Ruggeri, S.
#2: Journal: Cell.Mol.Life.Sci. / Year: 2003
Title: Pcf Protein from Phytophthora Cactorum and its Recombinant Homologue Elicit Phenylalanine Ammonia Lyase Activation in Tomato
Authors: Orsomando, G. / Lorenzi, M. / Ferrari, E. / Dechiara, C. / Spisni, A. / Ruggieri, S.
History
DepositionJan 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Revision 1.2Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHYTOTOXIC PROTEIN PCF


Theoretical massNumber of molelcules
Total (without water)5,6171
Polymers5,6171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
Representative

-
Components

#1: Protein PHYTOTOXIC PROTEIN PCF


Mass: 5617.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROLINE 49 IS HYDROXYLATED / Source: (gene. exp.) PHYTOPHTHORA CACTORUM (eukaryote) / Strain: P381 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: Q94FS7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
1212D-TOCSY
1312D-HSQC
1413D-TOCSY-HSQC
1513D-NOESY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE ON 15N-LABELED PCF

-
Sample preparation

DetailsContents: 90%WATER/10%D2O
Sample conditionsIonic strength: 10 mM / pH: 5.0 / Pressure: 1.0 atm / Temperature: 293.0 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
DiscoverBRUNGERrefinement
Discoverstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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