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- PDB-1kg1: NMR structure of the NIP1 elicitor protein from Rhynchosporium secalis -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Necrosis Inducing Protein 1


Theoretical massNumber of molelcules
Total (without water)6,4511
Polymers6,4511
Non-polymers00
Water0
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

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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

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Experimental details

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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

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM NIP1, 97% 15N incorporationH2O
22.0mM NIP1, unlabeledH2O
32.0mM NIP1, unlabeledD2O
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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

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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

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