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- PDB-1j9n: Solution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dG... -

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Basic information

Entry
Database: PDB / ID: 1j9n
TitleSolution Structure of the Nucleopeptide [AC-LYS-TRP-LYS-HSE(p3*dGCATCG)-ALA]-[p5*dCGTAGC]
Components
  • 5'-D(*CP*GP*TP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*AP*CP*(PGN))-3'
  • peptide ACE-LYS-TRP-LYS-HSE-ALA
KeywordsDNA BINDING PROTEIN/DNA / COVALENTLY LINKED PEPTIDE-DNA COMPLEX / TRYPTOPHAN STACKING / DNA BINDING PROTEIN-DNA COMPLEX
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics matrix relaxation
AuthorsGomez-Pinto, I. / Marchan, V. / Gago, F. / Grandas, A. / Gonzalez, C.
CitationJournal: Chembiochem / Year: 2003
Title: Solution structure and stability of tryptophan-containing nucleopeptide duplexes
Authors: Gomez-Pinto, I. / Marchan, V. / Gago, F. / Grandas, A. / Gonzalez, C.
History
DepositionMay 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*TP*AP*CP*(PGN))-3'
B: 5'-D(*CP*GP*TP*AP*GP*C)-3'
C: peptide ACE-LYS-TRP-LYS-HSE-ALA


Theoretical massNumber of molelcules
Total (without water)4,3593
Polymers4,3593
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)10 / 10all calculated structures submitted
RepresentativeModel #1

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Components

#1: DNA chain 5'-D(*GP*CP*TP*AP*CP*(PGN))-3'


Mass: 1889.198 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*AP*GP*C)-3'


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein/peptide peptide ACE-LYS-TRP-LYS-HSE-ALA


Mass: 660.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 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

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM nucleopeptide, 25 mM phosphate buffer, 100 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
22MM nucleopeptide, 25 mM phosphate buffer, 100 mM NaCl, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17 1 atm278 K
27 1 atm278 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 AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3brukercollection
MARDIGRAS5.2james, t.l.iterative matrix relaxation
DYANA1.5guntert, Pstructure solution
SANDER5kollman, p.refinement
RefinementMethod: molecular dynamics matrix relaxation / Software ordinal: 1
Details: the structures are based on a total of 276 NOE-derived distance constraints, and 33 dihedral angle restraints
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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