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- PDB-5w54: Cytokine-like Stress Response Peptide-2 in Manduca Sexta -

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Basic information

Entry
Database: PDB / ID: 5w54
TitleCytokine-like Stress Response Peptide-2 in Manduca Sexta
ComponentsStress Response Peptide-2
KeywordsCYTOKINE / Anti-Parallel Beta-strands / Disulfide Disordered
Function / homologyStress Response Peptide-2
Function and homology information
Biological speciesManduca sexta (tobacco hornworm)
MethodSOLUTION NMR / simulated annealing
AuthorsSchrag, L.G. / Herrera, A.I. / Prakash, O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58634 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112662 United States
CitationJournal: Protein Pept. Lett. / Year: 2017
Title: Solution Structure and Expression Profile of an Insect Cytokine: Manduca sexta Stress Response Peptide-2.
Authors: Schrag, L.G. / Cao, X. / Herrera, A.I. / Wang, Y. / Jiang, H. / Prakash, O.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3Jun 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

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Structure visualization

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Assembly

Deposited unit
A: Stress Response Peptide-2


Theoretical massNumber of molelcules
Total (without water)2,7581
Polymers2,7581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2870 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Stress Response Peptide-2


Mass: 2758.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Manduca sexta (tobacco hornworm) / References: UniProt: A0A2D0TCH0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D DQF-COSY
121anisotropic12D 1H-1H TOCSY
131anisotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 2.0 mM Stress Response Peptide-2, 90% H2O/10% D2O
Details: 10% Deuterium sample with ~2.0mM peptide concentration. No salt added.
Label: SRP2_10D20/90H20 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.0 mM / Component: Stress Response Peptide-2 / Isotopic labeling: natural abundance
Sample conditionsIonic strength units: Not defined / Label: SRP2@25C / pH: 2.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger A. T. et.al.refinement
Procheck3.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
VnmrJ3.2Variancollection
CNS1.3Brunger A. T. et.al.structure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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