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- PDB-1oo7: DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURIN... -

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Basic information

Entry
Database: PDB / ID: 1oo7
TitleDNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES
Components
  • 5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU)P*(PDU)P*C)-3'
  • 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'
KeywordsDNA-RNA HYBRID / DNA.RNA HYBRID / PURINE/PYRIMIDINE-RICH STRANDS / ANTISENSE / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / MULTIPLE STARTING CONFORMATIONS
Model type detailsminimized average
AuthorsGyi, J.I. / Gao, D. / Conn, G.L. / Trent, J.O. / Brown, T. / Lane, A.N.
Citation
Journal: Nucleic Acids Res. / Year: 2003
Title: The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications
Authors: Gyi, J.I. / Gao, D. / Conn, G.L. / Trent, J.O. / Brown, T. / Lane, A.N.
#1: Journal: Biochemistry / Year: 1998
Title: Solution Structures of DNA.RNA Hybrids with Purine-Rich and Pyrimidine-Rich Strands: Comparison with the Homologous DNA and RNA Duplexes
Authors: Gyi, J.I. / Lane, A.N. / Conn, G.L. / Brown, T.
#2: Journal: Biochemistry / Year: 1996
Title: Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes
Authors: Gyi, J.I. / Conn, G.L. / Lane, A.N. / Brown, T.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 28, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / pdbx_nmr_software / 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 / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 1, 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'
B: 5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU)P*(PDU)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,4832
Polymers6,4832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'


Mass: 3287.076 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU)P*(PDU)P*C)-3'


Mass: 3196.194 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED FROM 2D HOMONUCLEAR NMR EXPERIMENTS USING UNLABELLED SAMPLE

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Sample preparation

DetailsSolvent system: 100% D2O OR 90% H2O, 10% D2O
Sample conditionsIonic strength: 100 mM KCL / pH: 7 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber7CORNELL, W.D., ET AL.refinement
Felix95Biosymprocessing
NUCFITLane, A.N.data analysis
pfitConte, M.R., Bauer, C.J., Lane, A.N.data analysis
RefinementMethod: MULTIPLE STARTING CONFORMATIONS / Software ordinal: 1
Details: DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING ...Details: DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST-SQUARES/GRID SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). TEN DIFFERENT SETS OF UNIQUE RESTRAINTS GENERATED 10 STRUCTURES, THE AVERAGE OF WHICH SATISFIED THE EXPERIMENTALLY DERIVED FRACTION OF SOUTH STATE SUGARS BETTER THAN STRUCTURES GENERATED FROM A SINGLE SET OF RESTRAINTS. INTERNUCLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE-BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCE FIELD AND A DISTANCE DIELECTRIC CONSTANT.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 4 / Conformers submitted total number: 4

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