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- PDB-1n0a: Turn stability in beta-hairpin peptides: 3:5 type I G1 bulge turns -

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Basic information

Entry
Database: PDB / ID: 1n0a
TitleTurn stability in beta-hairpin peptides: 3:5 type I G1 bulge turns
Componentsbhpw_pdg, beta-hairpin peptide
KeywordsDE NOVO PROTEIN / beta hairpin / beta-turn / beta-bulge
MethodSOLUTION NMR / distance geometry, restrained molecular dynamics
AuthorsBlandl, T. / Cochran, A.G. / Skelton, N.J.
CitationJournal: PROTEIN SCI. / Year: 2003
Title: Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns
Authors: Blandl, T. / Cochran, A.G. / Skelton, N.J.
History
DepositionOct 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE There is no sequence database reference since the peptide is a de novo designed sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bhpw_pdg, beta-hairpin peptide


Theoretical massNumber of molelcules
Total (without water)1,2771
Polymers1,2771
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)21 / 80structures with the least restraint violations
RepresentativeModel #3closest to the average

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Components

#1: Protein/peptide bhpw_pdg, beta-hairpin peptide


Mass: 1277.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D ROESY
1212D TOCSY
131DQF-COSY
2422D ROESY
2522D COSY-35
2622D 13C-HMQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques augmented by loose phi and psi restraints generated from TALOS. MODEL 21 is the average minimized structure.

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Sample preparation

Details
Solution-IDContentsSolvent system
18 mM peptide, no buffer90% H2O/10% D2O
28 mM peptide, no buffer100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1051 atm303 K
2051 atm303 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 DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DGII98Tim Havelstructure solution
Discover3Accelrysrefinement
NMRPipe2001Frank Delagliodata analysis
Felix98Accelrysdata analysis
XwinNMR3.1Brukercollection
RefinementMethod: distance geometry, restrained molecular dynamics / Software ordinal: 1
Details: 100 distance geometry structures were calculated. The 80 structures of lowest penalty function were further refined using restrained molecular dynamics. The 20 structures of lowest restraint ...Details: 100 distance geometry structures were calculated. The 80 structures of lowest penalty function were further refined using restrained molecular dynamics. The 20 structures of lowest restraint violation energy were used to describe the structure. 61 distance and 21 dihedral angle restraints were used. The final ensemble has no distance violations greater than 0.1 A and no dihedral angle vioaltions greater than 1 degree. 95% of the residues are in the most favourable region of the Ramachandran plot. The mean backbone atom rmsd to the mean structure is 0.29+/-0.05 A.
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: 21

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