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- PDB-2oru: Solution structure of xtz1-peptide, a beta-hairpin peptide with a... -

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Entry
Database: PDB / ID: 2oru
TitleSolution structure of xtz1-peptide, a beta-hairpin peptide with a structured extension
Componentsxtz1-peptide
KeywordsDE NOVO PROTEIN / hairpin
MethodSOLUTION NMR / Simulated annealing, TORSION ANGLE DYNAMICS
AuthorsCampbell, R.E.
CitationJournal: Chembiochem / Year: 2007
Title: In Vivo Screening Identifies a Highly Folded beta-Hairpin Peptide with a Structured Extension.
Authors: Cheng, Z. / Miskolzie, M. / Campbell, R.E.
History
DepositionFeb 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: xtz1-peptide


Theoretical massNumber of molelcules
Total (without water)2,5521
Polymers2,5521
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide xtz1-peptide


Mass: 2551.854 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121DQF-COSY
1312D NOESY

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Sample preparation

DetailsContents: 2 mM xtz1-peptide; 90% H2O, 10% D2O, pH 6, 0.010 ml of 0.1% DSS
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 2 mM peptide / pH: 6 / Pressure: AMBIENT / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1ccollection
NMRView6.4Johnsonprocessing
CYANA2.1Guentertstructure solution
CYANA2.1Guentertrefinement
RefinementMethod: Simulated annealing, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: Chemical shift assignments were manually done. Automated NOESY assignment and structure ensemble calculation was performed with CYANA v.2.1. A total of 431 unassigned NOESY peaks with ...Details: Chemical shift assignments were manually done. Automated NOESY assignment and structure ensemble calculation was performed with CYANA v.2.1. A total of 431 unassigned NOESY peaks with intensity greater than ~1% of the most intense NOESY peak were input to CYANA. CYANA assigned 403 of 431 (93.5%) peaks, of which 309 were used as distance constraints in the structure calculation.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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