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- PDB-2lb4: DNA / RNA Hybrid containing a central stereo specific Sp borano p... -

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Basic information

Entry
Database: PDB / ID: 2lb4
TitleDNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkage
Components
  • DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_
  • RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_
KeywordsDNA/RNA / nucleic acid heteroduplex / RNase H1 activity / DNA-RNA complex
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsstructure with lowest restraint violations, model 1
AuthorsJohnson, C.N. / Spring, A.M. / Shaw, B.R. / Germann, M.W.
CitationJournal: Biochemistry / Year: 2011
Title: Structural Basis of the RNase H1 Activity on Stereo Regular Borano Phosphonate DNA/RNA Hybrids.
Authors: Johnson, C.N. / Spring, A.M. / Sergueev, D. / Shaw, B.R. / Germann, M.W.
History
DepositionMar 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_
B: RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_


Theoretical massNumber of molelcules
Total (without water)5,5982
Polymers5,5982
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 / 10structure with lowest restraint violations
RepresentativeModel #1structure with lowest restraint violations

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Components

#1: DNA chain DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_


Mass: 2743.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_


Mass: 2854.782 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
1112D 1H-1H NOESY
1222D 1H-13C HSQC
1322D 1H-1H TOCSY
1422D 1H-1H NOESY
1522D DQF-COSY
1622D 1H-31P CORR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS, 99.999 % D2O99.999 % D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMDNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')-11
1.0 mMRNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')-21
50 mMsodium chloride-31
10 mMsodium phosphate-41
0.5 mMEDTA-51
0.3 uMDSS-61
10 %D2O-71
90 %H2O-81
1.0 mMDNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')-92
1.0 mMRNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')-102
50 mMsodium chloride-112
10 mMsodium phosphate-122
0.5 mMEDTA-132
0.3 uMDSS-142
99.999 %D2O-152
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmgeometry optimization
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
XwinNMR3.5Bruker Biospincollection
TopSpin2.1Bruker Biospindata analysis
TopSpin2.1Bruker Biospinprocessing
CORMA5.21Thomas Jamesdata analysis
MARDIGRAS5.21Thomas Jamesrefinement
Sparky3.98Goddarddata analysis
Sparky3.98Goddardchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: structure with lowest restraint violations
NMR ensembleConformer selection criteria: structure with lowest restraint violations
Conformers calculated total number: 10 / Conformers submitted total number: 1

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