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- PDB-6gh0: Two-quartet kit* G-quadruplex is formed via double-stranded pre-f... -

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Basic information

Entry
Database: PDB / ID: 6gh0
TitleTwo-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure
ComponentsDNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3')
KeywordsDNA / G-quadruplex / two G-quartets / c-KIT promoter
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKotar, A. / Rigo, R. / Sissi, C. / Plavec, J.
Funding support Slovenia, Italy, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
CPDA147272/14 Italy
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure.
Authors: Kotar, A. / Rigo, R. / Sissi, C. / Plavec, J.
History
DepositionMay 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,9401
Polymers6,9401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4120 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 6940.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
118isotropic12D 1H-1H NOESY
128isotropic22D 1H-1H NOESY
135isotropic21D 1H-15N HSQC
145isotropic22D 1H-15N HSQC
155isotropic22D 1H-13C HSQC
267isotropic12D 1H-1H TOCSY
176isotropic12D 1H-13C HSQC aromatic
185isotropic22D 1H-15N HSQC NH2 only
297isotropic12D DQF-COSY
1106isotropic22D 1H-1H NOESY
1116isotropic12D 1H-1H NOESY
2127isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution50.5 mM 10% 13C, 10% 15N DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2OResidue specific labeling. In total 19 samples were prepared differing only in the position of the isotopically enriched residue.13C_15N_sample90% H2O/10% D2O
solution60.4 mM DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution70.4 mM DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 100% D2Osample_2100% D2O
solution80.5 mM DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2Osample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3')10% 13C, 10% 15N5
100 mMpotassium chloridenatural abundance5
20 mMpotassium phosphatenatural abundance5
0.4 mMDNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3')natural abundance6
100 mMpotassium chloridenatural abundance6
20 mMpotassium phosphatenatural abundance6
0.4 mMDNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3')natural abundance7
100 mMpotassium chloridenatural abundance7
20 mMpotassium phosphatenatural abundance7
0.5 mMDNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3')natural abundance8
100 mMpotassium chloridenatural abundance8
20 mMpotassium phosphatenatural abundance8
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMconditions_17.41 atm310 K
2100 mMconditions_27.8 pD1 atm310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System8001
Varian Uniform NMR SystemVarianUniform NMR System6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR3.2AVariancollection
VNMR3.2AVarianprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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