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- PDB-5oe1: Im polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides... -

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Basic information

Entry
Database: PDB / ID: 5oe1
TitleIm polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies
ComponentsDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
KeywordsDNA / Minor groove binders / hairpin poyamides
Function / homologyChem-9T8 / 1-methylimidazole-2-carboxylic acid / GAMMA-AMINO-BUTANOIC ACID / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics / matrix relaxation
AuthorsPadroni, G. / Parkinson, J. / Burley, G.A.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides.
Authors: Padroni, G. / Parkinson, J.A. / Fox, K.R. / Burley, G.A.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 8, 2019Group: Data collection
Category: chem_comp / pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _chem_comp.type / _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jul 13, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _audit_author.name / _chem_comp.type ..._audit_author.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,55112
Polymers7,1652
Non-polymers1,38610
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy, Tm and circular dichroism
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2340 Å2
ΔGint1 kcal/mol
Surface area4600 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 2000clustering
Representative

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 3582.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-9TK / 1-methylimidazole-2-carboxylic acid


Mass: 126.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O2
#3: Chemical
ChemComp-PYB / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID


Mass: 140.140 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8N2O2
#4: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#5: Chemical ChemComp-IMT / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID


Mass: 141.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N3O2
#6: Chemical ChemComp-9T8 / 3-(3-azaniumylpropanoylamino)propyl-dimethyl-azanium


Mass: 175.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H21N3O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
141isotropic12D 1H-1H TOCSY
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-31P COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8, 100% D2OPA8_D2O100% D2O
solution21.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8, 90% H2O/10% D2OPA8_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')natural abundance1
1.3 mMPA8natural abundance1
1.3 mMDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')natural abundance2
1.3 mMPA8natural abundance2
Sample conditionsIonic strength: 100 phosphate mM / Label: Standard / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
MARDIGRASN. Ulyanovstructure calculation
Refinement
MethodSoftware ordinal
molecular dynamics1
matrix relaxation5
NMR ensembleConformer selection criteria: clustering / Conformers calculated total number: 2000 / Conformers submitted total number: 10

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