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- PDB-6kra: Solution NMR Structure of RMAD4 alpha Defensin -

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Basic information

Entry
Database: PDB / ID: 6kra
TitleSolution NMR Structure of RMAD4 alpha Defensin
ComponentsNeutrophil defensin 4
KeywordsANTIMICROBIAL PROTEIN / Defensin / beta-sheets / disulfide bonds / antimicrobial
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / defense response to fungus / innate immune response in mucosa / 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 / extracellular space
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Neutrophil defensin 4
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodSOLUTION NMR / simulated annealing
AuthorsAgadi, N. / Kumar, A. / Shukla, V.K.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (India)SR/SO/BB-0022/2012 India
Department of Science & Technology (India)SR/WOS-A/LS-566/2013(G) India
CitationJournal: To Be Published
Title: Solution NMR Structure of RMAD4 alpha Defensin.
Authors: Agadi, N. / Kumar, A. / Shukla, V.K. / Vasudevan, S.V.
History
DepositionAug 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)3,9741
Polymers3,9741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Neutrophil defensin 4 / RMAD-4


Mass: 3973.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Macaca mulatta (Rhesus monkey) / References: UniProt: P82319

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM Rehesus macaque Myeloid Alpha Defensin 4, 0.01 % v/v Glacial Acetric acid, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O, 90% H2O/10% D2O
Details: Synthetic peptide was refolded using Air Oxidation and then purified by HPLC
Label: Natural Abundance / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRehesus macaque Myeloid Alpha Defensin 4natural abundance1
0.01 % v/vGlacial Acetric acidnatural abundance1
90 % v/vH2Onatural abundance1
10 % v/vD2O[U-99% 2H]1
Sample conditionsIonic strength: 0 Not defined / Label: natural abundance / pH: 3.7 / PH err: 0.05 / Pressure: 760 mmHg / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker Ascend / Manufacturer: Bruker / Model: Ascend / Field strength: 750 MHz / Details: IIT BOMBAY

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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