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- PDB-7wgw: NMR Solution Structure of a cGMP Fill-in Vacancy G-quadruplex For... -

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Basic information

Entry
Database: PDB / ID: 7wgw
TitleNMR Solution Structure of a cGMP Fill-in Vacancy G-quadruplex Formed in the Oxidized BLM Gene Promoter
ComponentsDNA (20-MER)
KeywordsDNA / 8-oxo-7 / 8-dihydroguanine / G-quadruplex / Bloom syndrome protein / guanine metabolite
Function / homologyCYCLIC GUANOSINE MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsWang, K.B. / Liu, Y. / Li, Y. / Li, J. / Dickerhoff, J. / Yang, M.H. / Yang, D. / Kong, L.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173707 China
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Oxidative Damage Induces a Vacancy G-Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G-Quadruplex in the Oxidized BLM Gene Promoter.
Authors: Wang, K.B. / Liu, Y. / Li, Y. / Dickerhoff, J. / Li, J. / Yang, M.H. / Yang, D. / Kong, L.Y.
History
DepositionDec 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: DNA (20-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6592
Polymers6,3141
Non-polymers3451
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1260 Å2
ΔGint13 kcal/mol
Surface area3900 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (20-MER)


Mass: 6314.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
331isotropic12D 1H-1H NOESY
441isotropic12D 1H-1H NOESY
551isotropic12D 1H-1H NOESY
161isotropic12D DQF-COSY
471isotropic12D 1H-13C HSQC
581isotropic12D 1H-13C HSQC
691isotropic12D 1H-1H NOESY
6101isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1.2 mM None BLM_G18O, 90% H2O/10% D2O / Label: none / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.2 mM / Component: BLM_G18O / Isotopic labeling: None
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_171 atm298 K
250 mMconditions_271 atm278 K
350 mMconditions_371 atm283 K
450 mMconditions_471 atm288 K
550 mMconditions_571 atm303 K
650 mMconditions_671 atm310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: QCI cryoprobe

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospinchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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