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- PDB-5mtg: G-quadruplex formed within promoters of Plasmodium falciparum B v... -

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Basic information

Entry
Database: PDB / ID: 5mtg
TitleG-quadruplex formed within promoters of Plasmodium falciparum B var genes - form I
ComponentsUpsB-Q-1 DNA (34-MER)
KeywordsDNA / G-quadruplex / nucleic acid / long loop / NMR spectroscopy / malaria
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / simulated annealing
AuthorsJuribasic Kulcsar, M. / Plavec, J.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
CitationJournal: To Be Published
Title: Stabilizing interactions in long-loop G-quadruplex formed within promoters of Plasmodium falciparum B var genes
Authors: Juribasic Kulcsar, M. / Gabelica, V. / Plavec, J.
History
DepositionJan 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 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 1.2Jun 19, 2019Group: Data collection
Category: pdbx_nmr_spectrometer / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_spectrometer.details / _pdbx_nmr_spectrometer.manufacturer / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 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

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Assembly

Deposited unit
A: UpsB-Q-1 DNA (34-MER)


Theoretical massNumber of molelcules
Total (without water)10,6651
Polymers10,6651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5930 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain UpsB-Q-1 DNA (34-MER)


Mass: 10664.855 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112anisotropic12D 1H-1H NOESY
123anisotropic12D 1H-1H NOESY
132anisotropic12D 1H-13C HMBC
141anisotropic22D 1H-15N HSQC
151anisotropic21D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM 8% 13C, 8% 15N UpsB-Q-1 DNA (34-MER), 150 mM potassium chloride, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution21.6 mM UpsB-Q-1 DNA (34-MER), 150 mM potassium chloride, 90% H2O/10% D2Ounlabeled sample90% H2O/10% D2O
solution31.8 mM UpsB-Q-1 DNA (34-MER), 150 mM potassium chloride, 100% D2Ounlabeled sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMUpsB-Q-1 DNA (34-MER)8% 13C, 8% 15N1
150 mMpotassium chloridenatural abundance1
1.6 mMUpsB-Q-1 DNA (34-MER)natural abundance2
150 mMpotassium chloridenatural abundance2
1.8 mMUpsB-Q-1 DNA (34-MER)natural abundance3
150 mMpotassium chloridenatural abundance3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian Uniform NMR SystemVarianUniform NMR System8001Agilent-Varian
Varian Uniform NMR SystemVarianUniform NMR System6002Agilent-Varian

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
VNMRVarianchemical shift assignment
SparkyGoddardpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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