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- PDB-1djf: NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE -

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Entry
Database: PDB / ID: 1djf
TitleNMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE
ComponentsGLN-ALA-PRO-ALA-TYR-LYS-LYS-ALA-ALA-LYS-LYS-LEU-ALA-GLU-SER
KeywordsDE NOVO PROTEIN / HYDROPHILIC AMPHIPATHIC BASIC HELIX PEPTIDE MODEL
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING, MOLECULAR DYNAMICS ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsMontserret, R. / McLeish, M.J. / Bockmann, A. / Geourjon, C. / Penin, F.
CitationJournal: Biochemistry / Year: 2000
Title: Involvement of electrostatic interactions in the mechanism of peptide folding induced by sodium dodecyl sulfate binding.
Authors: Montserret, R. / McLeish, M.J. / Bockmann, A. / Geourjon, C. / Penin, F.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: GLN-ALA-PRO-ALA-TYR-LYS-LYS-ALA-ALA-LYS-LYS-LEU-ALA-GLU-SER


Theoretical massNumber of molelcules
Total (without water)1,6081
Polymers1,6081
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)1 / 50restraint violation and low energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide GLN-ALA-PRO-ALA-TYR-LYS-LYS-ALA-ALA-LYS-LYS-LEU-ALA-GLU-SER


Mass: 1607.890 Da / Num. of mol.: 1 / Fragment: HUMAN PLATELET FACTOR 4, SEGMENT 56-70 / Mutation: L59A, I63A, I64A, L68A / Source method: obtained synthetically / Details: THIS MODEL PEPTIDE WAS CHEMICALLY SYNTHESIZED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
1411H-13C-HSQC
1511H-13C-HSQC-TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR AND 1H-13C HETERONUCLEAR METHODS.

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Sample preparation

DetailsContents: 10MM SODIUM PHOSPHATE BUFFER PH 6.0
Sample conditionsIonic strength: 10mM SODIUM PHOSPHATE / pH: 6 / Pressure: AMBIENT / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1VARIAN INC.collection
X-PLOR3.1BRUNGER, A.T.structure solution
X-PLOR3.1BRUNGER, A.T.refinement
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING, MOLECULAR DYNAMICS ENERGY MINIMIZATION
Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 136 RESTRAINTS, 126 OF WHICH BEING NOE- DERIVED DISTANCE CONSTRAINTS AND 10 DIHEDRAL ANGLE RESTRAINTS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: restraint violation and low energy
Conformers calculated total number: 50 / Conformers submitted total number: 1

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