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- PDB-5gwg: Solution structure of rattusin -

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Basic information

Entry
Database: PDB / ID: 5gwg
TitleSolution structure of rattusin
ComponentsDefensin alpha-related sequence 1
KeywordsANTIMICROBIAL PROTEIN / defensin antimicrobial peptide / cysteine-rich peptide / disulfide bond
Function / homology
Function and homology information


Defensins / Alpha-defensins / disruption of plasma membrane integrity in another organism / Neutrophil degranulation / innate immune response in mucosa / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular space
Similarity search - Function
Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide
Similarity search - Domain/homology
Defensin alpha-like protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsLee, C.W. / Min, H.J.
CitationJournal: Sci Rep / Year: 2017
Title: Rattusin structure reveals a novel defensin scaffold formed by intermolecular disulfide exchanges
Authors: Min, H.J. / Yun, H. / Ji, S. / Rajasekaran, G. / Kim, J.I. / Kim, J.S. / Shin, S.Y. / Lee, C.W.
History
DepositionSep 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 13, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin alpha-related sequence 1
B: Defensin alpha-related sequence 1


Theoretical massNumber of molelcules
Total (without water)7,3152
Polymers7,3152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1210 Å2
ΔGint-16 kcal/mol
Surface area5170 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Defensin alpha-related sequence 1 / rattusin / Protein Defal1


Mass: 3657.355 Da / Num. of mol.: 2 / Fragment: UNP residues 57-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Defal1, Defa-rs1, rCG_43351 / Production host: unidentified (others) / References: UniProt: Q4JEI2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H TOCSY
121anisotropic12D DQF-COSY
131anisotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 1.0 mM rattusin, 90% H2O/10% D2O / Label: refolded / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: rattusin / Isotopic labeling: natural abundance
Sample conditionsDetails: 10mM sodium phosphate / Ionic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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