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- PDB-2icz: NMR Structures of the Expanded DNA 10bp xTGxTAxCxGCxAxGT:xACTxGCG... -

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Basic information

Entry
Database: PDB / ID: 2icz
TitleNMR Structures of the Expanded DNA 10bp xTGxTAxCxGCxAxGT:xACTxGCGxTAxCA
Components
  • 5'-D(*(XAE)P*CP*TP*(XGA)P*CP*GP*(XTY)P*AP*(XCS)P*A)-3'
  • 5'-D(*(XTY)P*GP*(XTY)P*AP*(XCS)P*(XGA)P*CP*(XAE)P*(XGA)P*T)-3'
KeywordsDNA / Expanded DNA / xDNA
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics cartesian dynamics
AuthorsLynch, S.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Toward a Designed, Functioning Genetic System with Expanded-Size Base Pairs: Solution Structure of the Eight-Base xDNA Double Helix.
Authors: Lynch, S.R. / Liu, H. / Gao, J. / Kool, E.T.
History
DepositionSep 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 9, 2022Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*(XTY)P*GP*(XTY)P*AP*(XCS)P*(XGA)P*CP*(XAE)P*(XGA)P*T)-3'
B: 5'-D(*(XAE)P*CP*TP*(XGA)P*CP*GP*(XTY)P*AP*(XCS)P*A)-3'


Theoretical massNumber of molelcules
Total (without water)6,6182
Polymers6,6182
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)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*(XTY)P*GP*(XTY)P*AP*(XCS)P*(XGA)P*CP*(XAE)P*(XGA)P*T)-3'


Mass: 3374.396 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*(XAE)P*CP*TP*(XGA)P*CP*GP*(XTY)P*AP*(XCS)P*A)-3'


Mass: 3243.268 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM DNA, 20 mM Na phosphate; 90% H2O/10% D2O90% H2O/10% D2O 100% D2O
21.0 mM DNA, 20 mM Na phosphate; 100% D2O
Sample conditionsIonic strength: 20 mM NaP / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. etallstructure solution
VNMR6.1Ccollection
Sparky3.106Goddard, T. D., Huang, C. C., Ferrin, T. E.data analysis
CNS1.1Brunger A. T. etallrefinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics cartesian dynamics
Software ordinal: 1
Details: 635 NOE, 25 Hydrogen Bonds, 180 torsion angle restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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