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- PDB-1l4v: SOLUTION STRUCTURE OF SAPECIN -

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Basic information

Entry
Database: PDB / ID: 1l4v
TitleSOLUTION STRUCTURE OF SAPECIN
ComponentsSapecin
KeywordsANTIBIOTIC / ANTIBACTERIAL PROTEIN / INSECT DEFENSIN
Function / homology
Function and homology information


defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Defensin, insect / Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSarcophaga peregrina (fry)
MethodSOLUTION NMR / simulated annealing
AuthorsHanzawa, H. / Iwai, H. / Takeuchi, K. / Kuzuhara, T. / Komano, H. / Kohda, D. / Inagaki, F. / Natori, S. / Arata, Y. / Shimada, I.
CitationJournal: FEBS Lett. / Year: 1990
Title: 1H nuclear magnetic resonance study of the solution conformation of an antibacterial protein, sapecin.
Authors: Hanzawa, H. / Shimada, I. / Kuzuhara, T. / Komano, H. / Kohda, D. / Inagaki, F. / Natori, S. / Arata, Y.
History
DepositionMar 6, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sapecin


Theoretical massNumber of molelcules
Total (without water)4,0871
Polymers4,0871
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)18 / 100structures with the lowest energy
RepresentativeModel #12closest to the average

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Components

#1: Protein/peptide Sapecin


Mass: 4086.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sarcophaga peregrina (fry) / References: UniProt: P18313

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
131HOHAHA
141PE-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 3mM Sapecin / Solvent system: CD3OH
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: JEOL GSX / Manufacturer: JEOL / Model: GSX / Field strength: 500 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 366 restraints, 338 are NOE-derived distance constraints, 28 dihedral angle restraints,26 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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