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- PDB-6ee9: Cytokine-like Peptide Stress-response Peptide-1 from Manduca Sexta -

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Basic information

Entry
Database: PDB / ID: 6ee9
TitleCytokine-like Peptide Stress-response Peptide-1 from Manduca Sexta
ComponentsStress-response Peptide-1
KeywordsCYTOKINE / Epidermal Growth Factor / Hemolymph Protein / Insect Immunity / Phenoloxidase
Biological speciesManduca sexta (tobacco hornworm)
MethodSOLUTION NMR / simulated annealing
AuthorsSchrag, L.
CitationJournal: To be published
Title: NMR Solution Structure and Expression Profile of Stress Response Peptide-1: A Cytokine from Manduca sexta
Authors: Schrag, L. / Cao, X. / Al Souhail, Q. / Kanost, M. / Jiang, H. / Prakash, O.
History
DepositionAug 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 23, 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:
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Assembly

Deposited unit
X: Stress-response Peptide-1


Theoretical massNumber of molelcules
Total (without water)2,8181
Polymers2,8181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2800 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Stress-response Peptide-1


Mass: 2818.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Manduca sexta (tobacco hornworm)
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: 1.8 mM Stress-response Peptide-1, 90% H2O/10% D2O / Label: Stress-response Peptide-1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.8 mM / Component: Stress-response Peptide-1 / Isotopic labeling: natural abundance
Sample conditionsIonic strength units: Not defined / Label: Conditions_1 / pH: 2.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR3.2aVariancollection
VNMR3.2aVarianprocessing
CcpNMR2.4CCPNpeak picking
Analysis2.4CCPNchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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