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- PDB-1rme: DNA (5'-D(MCYP*CP*TP*CP*C)-3') tetramer, NMR, 1 structure -

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Basic information

Entry
Database: PDB / ID: 1rme
TitleDNA (5'-D(MCYP*CP*TP*CP*C)-3') tetramer, NMR, 1 structure
ComponentsDNA (5'-D(*(MCY)P*CP*TP*CP*C)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / I-MOTIF / TETRAMER
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsNonin, S. / Leroy, J.-L.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.
Authors: Nonin, S. / Leroy, J.L.
#1: Journal: Structure / Year: 1995
Title: Solution Structures of the I-Motif Tetramers of D(Tcc), D(5Methylcct) and D(T5Methylcc): Novel Noe Connections between Amino Protons and Sugar Protons
Authors: Leroy, J.L. / Gueron, M.
History
DepositionJul 12, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair_step.tilt ..._ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.twist / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_software.authors / _struct_conn.details / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,4004
Polymers5,4004
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3880 Å2
ΔGint-0 kcal/mol
Surface area2070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 24structures with the least restraint violations
Representative

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Components

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


Mass: 1350.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: TETRAMER FORMED BY FOUR 5MCCTCC STRANDS / 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
111NOESY
121TOCSY
1311H EXCHANGE
141NOESY-ROESY
152TOCSY
162NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution18 mM d(5mCCTCC), 90% H20/10% D2Osample_190% H2O/10% D2O
solution28 mM d(5mCCTCC), 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
8 mMd(5mCCTCC)1
8 mMd(5mCCTCC)2
Sample conditionspH: 4.6 / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built HOME MADE SPECTROMETERHome-builtHOME MADE SPECTROMETER3601
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 24 / Conformers submitted total number: 1

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