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- PDB-1bk8: DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF AESC... -

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Basic information

Entry
Database: PDB / ID: 1bk8
TitleDETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF AESCULUS HIPPOCASTANUM ANTIMICROBIAL PROTEIN 1 (AH-AMP1) BY 1H NMR, 25 STRUCTURES
ComponentsANTIMICROBIAL PROTEIN 1
KeywordsPLANT DEFENSIN / ANTIMICROBIAL / CYSTEINE-STABILIZED ALFA/ BETA MOTIF
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / extracellular region
Similarity search - Function
Gamma-thionin family / 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 1
Similarity search - Component
Biological speciesAesculus hippocastanum (common horse chestnut)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsFant, F. / Borremans, F.A.M.
CitationJournal: Proteins / Year: 1999
Title: The three-dimensional solution structure of Aesculus hippocastanum antimicrobial protein 1 determined by 1H nuclear magnetic resonance.
Authors: Fant, F. / Vranken, W.F. / Borremans, F.A.
History
DepositionJul 15, 1998Processing site: BNL
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIMICROBIAL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)5,8741
Polymers5,8741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 500LEAST RESTRAINT VIOLATION AND ENERGY
Representative

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Components

#1: Protein/peptide ANTIMICROBIAL PROTEIN 1 / AH-AMP1


Mass: 5873.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Aesculus hippocastanum (common horse chestnut)
Organ: SEED / References: UniProt: Q7M1F3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQFCOSY
141E.COSY
NMR detailsText: 2D HOMONUCLEAR 1H NMR WAS USED TO EXTRACT DISTANCE AND TORSIONAL CONSTRAINTS. RMSD BACKBONE ATOMS 0.81 +/- 0.12. RMSD ALL ATOMS 1.25 +/- 0.13. THE AMBER FORCEFIELD WAS USED FOR THE SIMULATED ANNEALING.

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Sample preparation

Sample conditionspH: 4.1 / Pressure: 1 atm / Temperature: 292.5 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM500 / Manufacturer: Bruker / Model: AM500 / Field strength: 500 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
DIANA/REDACstructure solution
Discoverstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: SIMULATED ANNEALING PROTOCOL ADOPTED FROM NILGES ET AL. 1988, FEBS LETTERS, VOL. 239, PP129-136.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND ENERGY
Conformers calculated total number: 500 / Conformers submitted total number: 25

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