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- PDB-2mrz: Dimeric structure of the Human A-box -

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Basic information

Entry
Database: PDB / ID: 2mrz
TitleDimeric structure of the Human A-box
ComponentsDNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')
KeywordsDNA / i-motif / centromere / self-recognition
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 10
AuthorsGaravis, M. / Escaja, N. / Gabelica, V. / Villasante, A. / Gonzalez, C.
CitationJournal: Chemistry / Year: 2015
Title: Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs.
Authors: Garavis, M. / Escaja, N. / Gabelica, V. / Villasante, A. / Gonzalez, C.
History
DepositionJul 18, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.pdbx_align_begin

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')
B: DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,8922
Polymers5,8922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')


Mass: 2945.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY

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Sample preparation

DetailsContents: 2.9 mM DNA-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.9 mM / Component: DNA-1
Sample conditionsIonic strength: 0 / pH: 3.6 / Pressure: ambient / Temperature: 278 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 softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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