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- PDB-1jbf: Hairpin Peptide that Inhibits IgE Activity by Binding to the High... -

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Basic information

Entry
Database: PDB / ID: 1jbf
TitleHairpin Peptide that Inhibits IgE Activity by Binding to the High Affinity IgE Receptor
ComponentsIGE06
KeywordsPROTEIN BINDING / beta-hairpin / type I turn
MethodSOLUTION NMR / Hybrid distance geometry, simulated annealing, restrained molecular dynamics.
AuthorsNakamura, G.R. / Starovasnik, M.A. / Reynolds, M.E. / Lowman, H.B.
CitationJournal: Biochemistry / Year: 2001
Title: A novel family of hairpin peptides that inhibit IgE activity by binding to the high-affinity IgE receptor.
Authors: Nakamura, G.R. / Starovasnik, M.A. / Reynolds, M.E. / Lowman, H.B.
History
DepositionJun 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGE06


Theoretical massNumber of molelcules
Total (without water)1,7761
Polymers1,7761
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 / 50structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide IGE06


Mass: 1776.090 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. It was based on naive phage-peptide library sorted for binding IgE receptor
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
1412D COSY-35
1512D ROESY
1622D NOESY
1722D COSY-35
NMR detailsText: 3JHNHa were obtained by fitting Lorentzian lines to the antiphase doublets of HN-Ha peaks in a 2QF-COSY spectrum processed to high digital resolution in F2. 3JHNHa for Gly8 and Gly11 were ...Text: 3JHNHa were obtained by fitting Lorentzian lines to the antiphase doublets of HN-Ha peaks in a 2QF-COSY spectrum processed to high digital resolution in F2. 3JHNHa for Gly8 and Gly11 were obtained from analysis of the COSY-35 spectrum acquired in H2O. 3JHaHb were extracted from a COSY-35 spectrum acquired in D2O.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM IGE0692% H2O/8% D2O, pH 5.7, 0.1 mM NaN3, 0.1 mM DSS
22 mM IGE06100% D2O, pH 5.7, 0.1 mM NaN3, 0.1 mM DSS
Sample conditionsIonic strength: no salt / pH: 5.7 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular Simulations, Inc.data analysis
UXNMRBruker, Inc.collection
DGII97Havelstructure solution
Discover97Molecular Simulations, Inc.refinement
RefinementMethod: Hybrid distance geometry, simulated annealing, restrained molecular dynamics.
Software ordinal: 1
Details: Structures were calculated based on a total of 109 distance and 16 dihedral angle restraints. The final ensemble of 20 models has no distance or dihedral angle restraint violations greater ...Details: Structures were calculated based on a total of 109 distance and 16 dihedral angle restraints. The final ensemble of 20 models has no distance or dihedral angle restraint violations greater than 0.1 angstrom or 2 degrees, respectively.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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