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- PDB-1nao: SOLUTION STRUCTURE OF AN RNA 2'-O-METHYLATED RNA DUPLEX CONTAININ... -

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Basic information

Entry
Database: PDB / ID: 1nao
TitleSOLUTION STRUCTURE OF AN RNA 2'-O-METHYLATED RNA DUPLEX CONTAINING AN RNA/DNA HYBRID SEGMENT AT THE CENTER, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • DNA/RNA (5'-R(*OMGP*OMUP*OMC)-D(P*AP*TP*CP*T)-R(P*OMCP*OMC)-3')
  • RNA (5'-R(*GP*GP*AP*GP*AP*UP*GP*AP*C)-3')
KeywordsDNA-RNA HYBRID / DNA/RNA DUPLEX
Function / homologyDNA/RNA hybrid / RNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsNishizaki, T. / Iwai, S. / Ohtsuka, E. / Nakamura, H.
CitationJournal: Biochemistry / Year: 1997
Title: Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center.
Authors: Nishizaki, T. / Iwai, S. / Ohtsuka, E. / Nakamura, H.
History
DepositionMar 29, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _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
Revision 1.4May 22, 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: RNA (5'-R(*GP*GP*AP*GP*AP*UP*GP*AP*C)-3')
B: DNA/RNA (5'-R(*OMGP*OMUP*OMC)-D(P*AP*TP*CP*T)-R(P*OMCP*OMC)-3')


Theoretical massNumber of molelcules
Total (without water)5,7382
Polymers5,7382
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 / 10AVERAGED
Representative

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Components

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


Mass: 2934.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: A SUBSTRATE OF RNASE H
#2: DNA/RNA hybrid DNA/RNA (5'-R(*OMGP*OMUP*OMC)-D(P*AP*TP*CP*T)-R(P*OMCP*OMC)-3')


Mass: 2802.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: A SUBSTRATE OF RNASE H

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: 00MM NACL, 50MM NA PHOSPHATE, 3MM EDTA

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR 3.1F3.1FBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGED / Conformers calculated total number: 10 / Conformers submitted total number: 1

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