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- PDB-2k4g: Solution Structure of a Peptide Nucleic Acid Duplex, 10 structures -

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Basic information

Entry
Database: PDB / ID: 2k4g
TitleSolution Structure of a Peptide Nucleic Acid Duplex, 10 structures
ComponentsPNA (N'-(*(GPN)*(GPN)*(CPN)*(APN)*(TPN)*(GPN)*(CPN)*(CPN))-C')
KeywordsPEPTIDE NUCLEIC ACID / PNA / PNA-PNA DUPLEX / left-handed duplex / P-FORM
Function / homologyMETHYLAMINE / DNA
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model type detailsminimized average
AuthorsHe, W. / Hatcher, E. / Balaeff, A. / Beratan, D. / Gil, R. / Madrid, M. / Achim, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations.
Authors: He, W. / Hatcher, E. / Balaeff, A. / Beratan, D.N. / Gil, R.R. / Madrid, M. / Achim, C.
History
DepositionJun 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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_nmr_spectrometer / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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: PNA (N'-(*(GPN)*(GPN)*(CPN)*(APN)*(TPN)*(GPN)*(CPN)*(CPN))-C')
B: PNA (N'-(*(GPN)*(GPN)*(CPN)*(APN)*(TPN)*(GPN)*(CPN)*(CPN))-C')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3784
Polymers4,3162
Non-polymers622
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 11all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain PNA (N'-(*(GPN)*(GPN)*(CPN)*(APN)*(TPN)*(GPN)*(CPN)*(CPN))-C')


Mass: 2158.187 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NME / METHYLAMINE


Mass: 31.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY

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Sample preparation

DetailsContents: 0.8 MM SS PNA, 10 MM SODIUM PHOSPHATE
Sample conditionspH: 7.0 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber9CASE, D. ET AL.refinement
Amber9CASE, D. ET AL.data analysis
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: MODEL 1 is the MINIMIZED AVERAGE OF 10 STRUCTURES (MODELS 2 TO 11). STRUCTURES HAVE NO MISSING ATOMS. HOWEVER, REMARK 470 and 610 WERE ADDED AUTOMATICALLY DUE TO PDB CONVENTIONS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 11 / Conformers submitted total number: 11

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