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- PDB-1le3: NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Pepti... -

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Basic information

Entry
Database: PDB / ID: 1le3
TitleNMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G
ComponentsTryptophan Zipper 4
KeywordsPROTEIN BINDING / Beta-hairpin / type I beta-turn
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
MethodSOLUTION NMR / Hybrid distance geometry, simulated annealing using the program DGII, , molecular dynamics using the program AMBER, in conjunction not only with distance, dihedral angle restraints, but also 1H chemical shift-based restraints.
AuthorsCochran, A.G. / Skelton, N.J. / Starovasnik, M.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Tryptophan zippers: stable, monomeric beta -hairpins.
Authors: Cochran, A.G. / Skelton, N.J. / Starovasnik, M.A.
#1: Journal: To be Published
Title: Chemical-shift-based methods for structure validation and refinement: Application to tryptophan zipper beta-hairpin peptides
Authors: Skelton, N.J. / Cochran, A.G. / Starovasnik, M.A.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 24, 2002ID: 1HS0
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan Zipper 4


Theoretical massNumber of molelcules
Total (without water)2,0121
Polymers2,0121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 64structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Tryptophan Zipper 4 / immunoglobulin G binding protein G


Mass: 2012.094 Da / Num. of mol.: 1 / Fragment: C-terminal hairpin of the B1 domain of Protein G / Mutation: Y45W/F52W/V54W / Source method: obtained synthetically
Details: This sequence is derived from residues 41-56 of the B1 domain of Protein G with three substitutions from the natural sequence, Y45W/F52W/V54W. The peptide was synthesized chemically.
References: UniProt: P06654

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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-ROESY
1412D-TOCSY
152COSY-35
NMR detailsText: The structure of trpzip4 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle ...Text: The structure of trpzip4 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle restraints were derived from analysis of NOESY, ROESY, DQF-COSY, and COSY-35 data. Chi-1 rotamers and stereospecific assignments for beta-methylene groups were based on combined analysis of 3JHaHb and local ROEs, suggesting that all four Trp residues adopt a chi1 of -60 deg. Quantitative analysis of the 1H chemical shifts, however, revealed that the frequencies of the Hb and He3 resonances of Trp5 and Trp14 were inconsistent with a -60 deg chi1 value, and indicated that the side chains for these tryptophans actually reside primarily in the 180 deg chi1 rotamer (Skelton et al., manuscript in preparation). The current coordinates result from refinement with the Sander module of AMBER (v6.0), and included not only NOE-derived distance restraints and dihedral angle restraints, but also 1H chemical shift-based restraints. Thus, the resulting updated coordinates differ from the previous ones in the side chain orientations of Trp5 and Trp14. However, the rest of the structure is similar with a backbone rmsd between the average coordinates of the two ensembles of 0.72 angstrom(res.43-54). The two strands are highly twisted, as described previously, however there is a slight difference in the relative position of the turn with respect to the strands. The key difference, however, is that each pair of cross-strand tryptophan rings now shows edge-to-face packing against one another. This sort of packing is observed for all tryptophan zipper peptides, regardless of turn type.

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Sample preparation

DetailsContents: 2mM trpzip4 / Solvent system: 92% H2O, 8% D2O, pH 6.0, 0.1mM DSS
Sample conditionsIonic strength: 0 / pH: 6.0 / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
Felix98Molecular Simulations, Inc.data analysis
DGII98Molecular Simulations, Inc.structure solution
Amber6Case and Kollmanrefinement
RefinementMethod: Hybrid distance geometry, simulated annealing using the program DGII, , molecular dynamics using the program AMBER, in conjunction not only with distance, dihedral angle restraints, but also ...Method: Hybrid distance geometry, simulated annealing using the program DGII, , molecular dynamics using the program AMBER, in conjunction not only with distance, dihedral angle restraints, but also 1H chemical shift-based restraints.
Software ordinal: 1
Details: Structures are based on a total of 130 (including 29 intra-residue, 30 sequential, 20 medium-range, and 51 long-range) NOE-derived distance restraints, 22 dihedral angle restraints, and 1H ...Details: Structures are based on a total of 130 (including 29 intra-residue, 30 sequential, 20 medium-range, and 51 long-range) NOE-derived distance restraints, 22 dihedral angle restraints, and 1H chemical shift restraints for 46 carbon-bound 1H resonances; (chemical shift restraints were not imposed for the terminal residues, or for side chains exhibiting evidence of rotational averaging). The ensemble agrees well with the experimental restraints with no distance or dihedral angle violations greater than 0.10 angstrom or 5 deg, respectively, and an average rmsd of only 0.106 ppm between observed and calculated chemical shifts.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 64 / Conformers submitted total number: 20

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