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- PDB-8psh: HIGH RESOLUTION NMR STRUCTURE OF THE STEREOREGULAR (ALL-RP)-PHOSP... -

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Basic information

Entry
Database: PDB / ID: 8psh
TitleHIGH RESOLUTION NMR STRUCTURE OF THE STEREOREGULAR (ALL-RP)-PHOSPHOROTHIOATE-DNA/RNA HYBRID D (G*PS*C*PS*G*PS*T*PS*C*PS*A*PS*G*PS*G)R(CCUGACGC), MINIMIZED AVERAGE STRUCTURE
Components
  • DNA (5'-D(*DGP*(SC)P*(GS)P*(PST)P*(SC)P*(AS)P*(GS)P*(GS))-3')
  • RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3')
KeywordsDNA-RNA HYBRID / OLIGONUCLEOTIDE / PHOSPHOROTHIOATE / THIONUCLEOTIDE / ANTISENSE
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsBachelin, M. / Hessler, G. / Kurz, G. / Hacia, J.G. / Dervan, P.B. / Kessler, H.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of a Stereoregular Phosphorothioate DNA/RNA Duplex
Authors: Bachelin, M. / Hessler, G. / Kurz, G. / Hacia, J.G. / Dervan, P.B. / Kessler, H.
History
DepositionOct 13, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DGP*(SC)P*(GS)P*(PST)P*(SC)P*(AS)P*(GS)P*(GS))-3')
B: RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0822
Polymers5,0822
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)1 / 50AVERAGE OF ALL STRUCTURES
Representative

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Components

#1: DNA chain DNA (5'-D(*DGP*(SC)P*(GS)P*(PST)P*(SC)P*(AS)P*(GS)P*(GS))-3')


Mass: 2580.090 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3')


Mass: 2501.553 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
121P.E.COSY
131TOCSY
141P-H COSY

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Sample preparation

Sample conditionspH: 7 / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6006001
Bruker DMX600BrukerDMX6005002
Bruker AMX500BrukerAMX5005003

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.97MSIrefinement
BRUKER UXNMRUXNMRstructure solution
TRIAD SYBYLSYBYLstructure solution
MARDIGRASstructure solution
MSI INSIGHT IIIIstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE OF ALL STRUCTURES / Conformers calculated total number: 50 / Conformers submitted total number: 1

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