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- PDB-1jxc: Minimized NMR structure of ATT, an Arabidopsis trypsin/chymotryps... -

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Basic information

Entry
Database: PDB / ID: 1jxc
TitleMinimized NMR structure of ATT, an Arabidopsis trypsin/chymotrypsin inhibitor
ComponentsPutative trypsin inhibitor ATTI-2
KeywordsHYDROLASE INHIBITOR / ATT / trypsin inhibitor / chymotrypsin inhibitor / Structural Genomics / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


secretory vesicle / sodium channel inhibitor activity / defense response to fungus / serine-type endopeptidase inhibitor activity / defense response / killing of cells of another organism / extracellular region
Similarity search - Function
Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defensin-like protein 195
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsZhao, Q. / Chae, Y.K. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Biochemistry / Year: 2002
Title: NMR Solution Structure of ATTp, an Arabidopsis thaliana Trypsin Inhibitor
Authors: Zhao, Q. / Chae, Y.K. / Markley, J.L.
History
DepositionSep 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative trypsin inhibitor ATTI-2


Theoretical massNumber of molelcules
Total (without water)7,4511
Polymers7,4511
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)1 / -
Representativeminimized average structure

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Components

#1: Protein Putative trypsin inhibitor ATTI-2


Mass: 7451.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATTp / Plasmid: pSNHisATT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q42328
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HN(CA)CB
141C(CO)NH SE
1513D 15N-separated NOESY
1613D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 15N 13C ATT 50 mM sodium perdeuterated acetate 0.1 mM DSS90% H2O/10% D2O
21mM 15N ATT 50 mM sodium perdeuterated acetate 0.1 mM DSS90% H2O/10% D2O
31mM ATT 50 mM sodium perdeuterated acetate 0.1 mM DSS90% H2O/10% D2O
41mM ATT 50 mM sodium perdeuterated acetate 0.1 mM DSS99.9% D2O
Sample conditionspH: 5 / Pressure: 1 atm / 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 DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionClassification
DYANA1.5structure solution
XwinNMRcollection
Felixprocessing
Sparkydata analysis
XEASYdata analysis
DYANA1.5refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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