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- PDB-2mit: Solution structure of oxidized dimeric form of human defensin 5 -

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Basic information

Entry
Database: PDB / ID: 2mit
TitleSolution structure of oxidized dimeric form of human defensin 5
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / cysteine knot / antimicrobial peptide
Function / homology
Function and homology information


positive regulation of membrane permeability / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / secretory granule / positive regulation of interleukin-8 production ...positive regulation of membrane permeability / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / secretory granule / positive regulation of interleukin-8 production / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / midbody / antibacterial humoral response / protein homotetramerization / secretory granule lumen / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / intracellular membrane-bounded organelle / innate immune response / protein homodimerization activity / extracellular space / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model1
AuthorsWommack, A.J. / Ziarek, J.J. / Wagner, G. / Nolan, E.M.
CitationJournal: To be Published
Title: Solution structure of oxidized dimeric form of human defensin 5
Authors: Wommack, A.J. / Ziarek, J.J. / Wagner, G. / Nolan, E.M.
History
DepositionDec 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin-5
B: Defensin-5


Theoretical massNumber of molelcules
Total (without water)7,1882
Polymers7,1882
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)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Defensin-5 / / Defensin / alpha 5 / HD5(63-94)


Mass: 3594.228 Da / Num. of mol.: 2 / Fragment: residues 63-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEF5, DEFA5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01523

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D HCACO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D C(CO)NH
1813D H(CCO)NH
1913D HNHB
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11222D 1H-15N HSQC
11322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-99% 13C; U-99% 15N] protein, 0.3 mM protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-99% 13C; U-99% 15N]1
0.3 mMentity-2[U-99% 13C; U-99% 15N]2
0.3 mMentity-32
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Varian AvanceVarianAvance5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CYANAGuntert, Mumenthaler and Wuthrichchemical shift calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
WhatIFVriendrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Initial structures calculated by minimizing target function. Final CYANA structure refined in explicit water using molecular dynamics.
NMR constraintsNOE constraints total: 1113 / NOE intraresidue total count: 270 / NOE long range total count: 384 / NOE medium range total count: 118 / NOE sequential total count: 232 / Disulfide bond constraints total count: 18 / Protein chi angle constraints total count: 28 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 38
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: 20 / Maximum torsion angle constraint violation: 3.3 ° / Maximum upper distance constraint violation: 0.66 Å
NMR ensemble rmsDistance rms dev: 0.0264 Å / Distance rms dev error: 0.0042 Å

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