[English] 日本語
Yorodumi
- PDB-1kg1: NMR structure of the NIP1 elicitor protein from Rhynchosporium secalis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kg1
TitleNMR structure of the NIP1 elicitor protein from Rhynchosporium secalis
ComponentsNecrosis Inducing Protein 1
KeywordsTOXIN / antiparalel beta sheets
Function / homology
Function and homology information


SH3 type barrels. - #460 / Rhinovirus 14, subunit 4 - #10 / Necrosis inducing protein-1 / Necrosis inducing protein-1 superfamily / Necrosis inducing protein-1 / Rhinovirus 14, subunit 4 / Other non-globular / Special / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesRhynchosporium secalis (leaf blotch of barley)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVan't Slot, K.A. / Van den Burg, H.A. / Kloks, C.P. / Hilbers, C.W. / Knogge, W. / Papavoine, C.H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Solution Structure of the Plant Disease Resistance-triggering Protein NIP1 from the Fungus Rhynchosporium secalis Shows a Novel beta-Sheet Fold.
Authors: Van't Slot, K.A. / Van Den Burg, H.A. / Kloks, C.P. / Hilbers, C.W. / Knogge, W. / Papavoine, C.H.
History
DepositionNov 26, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Necrosis Inducing Protein 1


Theoretical massNumber of molelcules
Total (without water)6,4511
Polymers6,4511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Necrosis Inducing Protein 1 / NIP1


Mass: 6451.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhynchosporium secalis (leaf blotch of barley)
Gene: Nip1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 / References: UniProt: Q02039
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
131HNHB
1422D NOESY
1532D NOESY
162DQF-COSY
171HMQC-NOESY-HMQC
181HMQC-NOESY-HMQC
1912D HMQC-J
1103DQF-COSY
NMR detailsText: Disulfide bond pattern was determined independently

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM NIP1, 97% 15N incorporationH2O
22.0mM NIP1, unlabeledH2O
32.0mM NIP1, unlabeledD2O
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertstructure solution
NMRPipeversion 1.8 Rev 2001.030.21.27Delaglioprocessing
XEASY1.3.13Bartelsdata analysis
DYANA1.5Guntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are besed on a total of 785 restraints: 740 NOE restraints and 45, 40 torsion angle restraints and 5 disulfide bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 25

+
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