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- PDB-1kvg: EPO-3 beta Hairpin Peptide -

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Basic information

Entry
Database: PDB / ID: 1kvg
TitleEPO-3 beta Hairpin Peptide
ComponentsProtein: EPO-3 Receptor Agonist
KeywordsDE NOVO PROTEIN / beta hairpin peptide
MethodSOLUTION NMR / distance geometry, restrained molecular dynamics
AuthorsSkelton, N.J. / Russell, S. / de Sauvage, F. / Cochran, A.G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Amino Acid Determinants of beta-Hairpin Conformation in Erythropoeitin Receptor Agonist Peptides Derived from a Phage Display Library
Authors: Skelton, N.J. / Russell, S. / de Sauvage, F. / Cochran, A.G.
#1: Journal: Biochemistry / Year: 1998
Title: Identification of a 13 amino acid peptide mimetic of erythropoietin and description of amino acids critical for the mimetic activity of EMP1
Authors: Johnson, D.L. / Farrell, F.X. / Barbone, F.P. / McMahon, F.J. / Tullai, J. / Hoey, K. / Livnah, O. / Wrighton, N.C. / Middleton, S.A. / Loughney, D.A. / Dower, W.J. / Mulcahy, L.S. / Wilson, ...Authors: Johnson, D.L. / Farrell, F.X. / Barbone, F.P. / McMahon, F.J. / Tullai, J. / Hoey, K. / Livnah, O. / Wrighton, N.C. / Middleton, S.A. / Loughney, D.A. / Dower, W.J. / Mulcahy, L.S. / Wilson, I.A. / Jolliffe, L.K.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AN APPROPRIATE DATABASE MATCH WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein: EPO-3 Receptor Agonist


Theoretical massNumber of molelcules
Total (without water)1,3341
Polymers1,3341
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 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Protein: EPO-3 Receptor Agonist


Mass: 1333.604 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is a novel sequence derived from phage-display selection.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-ROESY
121DQF-COSY
2322D-ROESY
242COSY-35
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
18 mM peptide90% H2O/10% D2O
28 mM peptide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 5.1 ambient 290 K
20 5.1 ambient 290 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 AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DGII98Timothy Havelstructure solution
Discover3.1Accelrysrefinement
RefinementMethod: distance geometry, restrained molecular dynamics / Software ordinal: 1
Details: The structures are based on 70 NOE distance restraints, 8 phi and 3 chi-1 dihedral angle restraints. No hydrogen bond restraints were employed. Note that the Ha-Hb coupling constants ...Details: The structures are based on 70 NOE distance restraints, 8 phi and 3 chi-1 dihedral angle restraints. No hydrogen bond restraints were employed. Note that the Ha-Hb coupling constants indicate rotational averaging about the Phe4 chi-1 angle. Several NOEs to the aromatic ring of Phe4 were not used to generate restraints as they could be satisfied by a -60 or 180 degree rotamer, but not by both. The mean backbone atom RMSD to the mean structure within the disulfide cycle is 0.31 +/- 0.06 Angstoms.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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