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- PDB-7rc8: Solution NMR Structure of [D-Ala19]Crp4 -

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Basic information

Entry
Database: PDB / ID: 7rc8
TitleSolution NMR Structure of [D-Ala19]Crp4
ComponentsAlpha-defensin 4Alpha defensin
KeywordsANTIMICROBIAL PROTEIN / cryptdin
Function / homology
Function and homology information


pore-forming activity / disruption of plasma membrane integrity in another organism / azurophil granule / transport vesicle / innate immune response in mucosa / phospholipid binding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / killing of cells of another organism / cellular response to lipopolysaccharide ...pore-forming activity / disruption of plasma membrane integrity in another organism / azurophil granule / transport vesicle / innate immune response in mucosa / phospholipid binding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / protein homodimerization activity / extracellular space
Similarity search - Function
Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsConibear, A.C. / Rosengren, K.J.
CitationJournal: Peptide Science / Year: 2022
Title: A conserved beta-bulge glycine residue facilitates folding and increases stability of the mouse alpha-defensin cryptdin-4
Authors: Clark, R.J. / Phan, T.H. / Song, A. / Ouellette, A.J. / Conibear, A.C. / Rosengren, K.J.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-defensin 4


Theoretical massNumber of molelcules
Total (without water)3,7861
Polymers3,7861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Structure is consistent with all experimental data
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Alpha-defensin 4 / Alpha defensin / Defensin-related cryptdin-4


Mass: 3785.636 Da / Num. of mol.: 1 / Mutation: G19DAL / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P28311

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
142isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC
162isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mg/mL [D-Ala19]Crp4, 1 mM DSS, 90% H2O/10% D2O[D-Ala19]Crp4 H2O/D2O90% H2O/10% D2O
solution21 mg/mL [D-Ala19]Crp4, 1 mM DSS, 100% D2O[D-Ala19]Crp4 D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mL[D-Ala19]Crp4natural abundance1
1 mMDSSnatural abundance1
1 mg/mL[D-Ala19]Crp4natural abundance2
1 mMDSSnatural abundance2
Sample conditionsIonic strength: 0 mM / Label: Standard 298K / pH: 4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospinprocessing
Refinement
MethodSoftware ordinalDetails
simulated annealing3using torsion angle dynamics
simulated annealing4using torsion angle dynamics and Cartesian space
simulated annealing5structures minimized in explicit water using Cartesian dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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