[English] 日本語
Yorodumi
- PDB-2kcn: Solution structure of the antifungal protein PAF from Penicillium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kcn
TitleSolution structure of the antifungal protein PAF from Penicillium chrysogenum
ComponentsAntifungal proteinAntifungal protein family
KeywordsANTIFUNGAL PROTEIN / antifungal protein PAF
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism
Similarity search - Function
Antifungal protein domain / Antifungal protein / Antifungal protein domain superfamily / Antifungal protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPenicillium chrysogenum (fungus)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 4
AuthorsBatta, G. / Barna, T. / Gaspari, Z. / Sandor, S. / Kover, K.E. / Binder, U. / Sarg, B. / Kaiserer, L. / Chhillar, A.K. / Eigentler, A. ...Batta, G. / Barna, T. / Gaspari, Z. / Sandor, S. / Kover, K.E. / Binder, U. / Sarg, B. / Kaiserer, L. / Chhillar, A.K. / Eigentler, A. / Leiter, E. / Hegedus, N. / Pocsi, I. / Lindner, H. / Marx, F.
CitationJournal: Febs J. / Year: 2009
Title: Functional aspects of the solution structure and dynamics of PAF--a highly-stable antifungal protein from Penicillium chrysogenum
Authors: Batta, G. / Barna, T. / Gaspari, Z. / Sandor, S. / Kover, K.E. / Binder, U. / Sarg, B. / Kaiserer, L. / Chhillar, A.K. / Eigentler, A. / Leiter, E. / Hegedus, N. / Pocsi, I. / Lindner, H. / Marx, F.
History
DepositionDec 23, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifungal protein


Theoretical massNumber of molelcules
Total (without water)6,2631
Polymers6,2631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Antifungal protein / Antifungal protein family


Mass: 6263.099 Da / Num. of mol.: 1 / Fragment: UNP residues 38-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: paf / References: UniProt: Q01701

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
NMR detailsText: The structure was determined from the 2D NOESY (130ms mixing time) using ATNOS/CANDID/CYANA 2.0

-
Sample preparation

DetailsContents: 1.6mM [U-100% 15N] PAF-1, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.6 mM / Component: PAF-1 / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 0.04 / pH: 5.0 / Pressure: ambient / Temperature: 304 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX7002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2Herrmann, Guntert, Wuthrichautomated noe chemical shift assignment
CYANA2Herrmann, Guntert, Wuthrichnmr structure calculation
CYANA2Herrmann, Guntert, Wuthrichmolecular dynamics calculation
CYANA2Herrmann, Guntert, Wuthrichprotein structure data analysis
CYANA2Herrmann, Guntert, Wuthrichchemical shift assignment
CYANA2Herrmann, Guntert, Wuthrichcollection
CYANA2Herrmann, Guntert, Wuthrichrefinement
CYANA2Guntert, Mumenthaler, Wuthrichautomated noe chemical shift assignment
CYANA2Guntert, Mumenthaler, Wuthrichnmr structure calculation
CYANA2Guntert, Mumenthaler, Wuthrichmolecular dynamics calculation
CYANA2Guntert, Mumenthaler, Wuthrichprotein structure data analysis
CYANA2Guntert, Mumenthaler, Wuthrichchemical shift assignment
CYANA2Guntert, Mumenthaler, Wuthrichcollection
CYANA2GROMACS, Bekker, Berendse, Dijkstraautomated noe chemical shift assignment
CYANA2GROMACS, Bekker, Berendse, Dijkstranmr structure calculation
CYANA2GROMACS, Bekker, Berendse, Dijkstramolecular dynamics calculation
CYANA2GROMACS, Bekker, Berendse, Dijkstraprotein structure data analysis
CYANA2GROMACS, Bekker, Berendse, Dijkstrachemical shift assignment
CYANA2GROMACS, Bekker, Berendse, Dijkstracollection
CYANA2Laskowski, MacArthurautomated noe chemical shift assignment
CYANA2Laskowski, MacArthurnmr structure calculation
CYANA2Laskowski, MacArthurmolecular dynamics calculation
CYANA2Laskowski, MacArthurprotein structure data analysis
CYANA2Laskowski, MacArthurchemical shift assignment
CYANA2Laskowski, MacArthurcollection
CYANA2Goddardautomated noe chemical shift assignment
CYANA2Goddardnmr structure calculation
CYANA2Goddardmolecular dynamics calculation
CYANA2Goddardprotein structure data analysis
CYANA2Goddardchemical shift assignment
CYANA2Goddardcollection
CYANA2Bruker Biospinautomated noe chemical shift assignment
CYANA2Bruker Biospinnmr structure calculation
CYANA2Bruker Biospinmolecular dynamics calculation
CYANA2Bruker Biospinprotein structure data analysis
CYANA2Bruker Biospinchemical shift assignment
CYANA2Bruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20 / Representative conformer: 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