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- PDB-2n30: Structure of Ace-pvhct-NH2 -

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Basic information

Entry
Database: PDB / ID: 2n30
TitleStructure of Ace-pvhct-NH2
ComponentsHemocyanin subunit L2
KeywordsANTIFUNGAL PROTEIN
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain ...Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Hemocyanin subunit L2
Similarity search - Component
Biological speciesLitopenaeus vannamei (Pacific white shrimp)
MethodSOLUTION NMR / simulated annealing
AuthorsPetit, V.W. / Rolland, J. / Blond, A. / Djediat, C. / Peduzzi, J. / Goulard, C. / Bachere, E. / Dupont, J. / Destoumieux-Garzon, D. / Rebuffat, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: A hemocyanin-derived antimicrobial peptide from the penaeid shrimp adopts an alpha-helical structure that specifically permeabilizes fungal membranes.
Authors: Petit, V.W. / Rolland, J.L. / Blond, A. / Cazevieille, C. / Djediat, C. / Peduzzi, J. / Goulard, C. / Bachere, E. / Dupont, J. / Destoumieux-Garzon, D. / Rebuffat, S.
History
DepositionMay 19, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemocyanin subunit L2


Theoretical massNumber of molelcules
Total (without water)2,7821
Polymers2,7821
Non-polymers00
Water00
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Hemocyanin subunit L2


Mass: 2782.099 Da / Num. of mol.: 1 / Fragment: UNP residues 654-676 / Source method: obtained synthetically
Source: (synth.) Litopenaeus vannamei (Pacific white shrimp)
References: UniProt: A0A059TFW7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 3.5 mM [U-99% 2H] peptide, methanol / Solvent system: methanol
SampleConc.: 3.5 mM / Component: peptide-1 / Isotopic labeling: [U-99% 2H]
Sample conditionsPressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR3.1Bruker Biospinprocessing
XWINNMR3.1Bruker Biospinchemical shift assignment
TOPSPIN3.2Bruker Biospinprocessing
TOPSPIN3.2Bruker Biospinchemical shift assignment
AURELIA3.8Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerpeak picking
AURELIA3.8Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerdata analysis
X-PLOR3.851Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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