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- PDB-6dxm: NMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGG) -

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Basic information

Entry
Database: PDB / ID: 6dxm
TitleNMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGG)
Components
  • DNA (5'-D(*CP*CP*CP*CP*GP*CP*CP*CP*A)-3')
  • DNA (5'-D(*TP*GP*GP*GP*CP*GP*GP*GP*G)-3')
KeywordsDNA / Sp1 Consensus Sequence
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDavis, E.V. / Hennig, M. / Arya, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM097917 United States
CitationJournal: To Be Published
Title: An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences
Authors: Davis, E.V. / Hennig, M. / Arya, D.P.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 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(*TP*GP*GP*GP*CP*GP*GP*GP*G)-3')
B: DNA (5'-D(*CP*CP*CP*CP*GP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,4752
Polymers5,4752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: UV Thermal Denaturation, CD spectroscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area3640 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 2852.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Watson-Crick DNA duplex chain A / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*CP*CP*CP*GP*CP*CP*CP*A)-3')


Mass: 2621.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Watson-Crick DNA duplex chain B / 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
111isotropic12D DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-1H NOESY
152isotropic22D 1H-1H NOESY
161isotropic22D ECOSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 100% D2Oequal molar eq. d(TGGGCGGGG).d(CCCCGCCCA) 100% D2O 25 mM NaCl, 5.0 mM Na Phosphate, 0.5 mM EDTA pH 7.0non-exchange100% D2O
solution2900 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 90% H2O/10% D2Oequal molar eq. d(TGGGCGGGG).d(CCCCGCCCA) 90% H2O /10% D2O 25 mM NaCl, 5.0 mM Na Phosphate, 0.5 mM EDTA pH 7.0exchange90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMDNAnatural abundance1
25 mMsodium chloridenatural abundance1
5 mMNa Phosphatenatural abundance1
0.5 mMEDTAnatural abundance1
900 uMDNAnatural abundance2
25 mMsodium chloridenatural abundance2
5 mMNa Phosphatenatural abundance2
0.5 mMEDTAnatural abundance2
Sample conditionsDetails: all nmr experiments / Ionic strength: 30 mM Na+ mM / Label: general / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
3DNALudata analysis
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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