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- PDB-2lo5: Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Reco... -

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Basic information

Entry
Database: PDB / ID: 2lo5
TitleStructural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA, Structure of a Thymine bulge
ComponentsDNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3')
KeywordsDNA / thymine bulge / hairpin / Bifunctional Zn(II) Macrocyclic Complex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model 1
AuthorsMorrow, J.R. / Fountain, M.A. / del Mundo, I.A. / Siter, K.E.
CitationJournal: Inorg.Chem. / Year: 2012
Title: Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA.
Authors: Del Mundo, I.M. / Siters, K.E. / Fountain, M.A. / Morrow, J.R.
History
DepositionJan 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,6641
Polymers3,6641
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)18 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 3664.380 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR structure of a d(GGCCGCAGTGCC)sequence
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2412D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3'), 100% D2O100% D2O
21.8 mM DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3'), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.8 mMDNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3')-11
1.8 mMDNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3')-22
Sample conditions
Conditions-IDIonic strengthPressure (kPa)Temperature (K)
10.1ambient 298 K
20.1ambient 288 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
Sparky3.14Goddardchemical shift assignment
Sparky3.14Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 6 / NA beta-angle constraints total count: 7 / NA chi-angle constraints total count: 6 / NA delta-angle constraints total count: 11 / NA epsilon-angle constraints total count: 6 / NA gamma-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 118 / NOE long range total count: 64
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 2.76 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 18 / Maximum lower distance constraint violation: 0.39 Å / Maximum torsion angle constraint violation: 4.1 ° / Maximum upper distance constraint violation: 0.25 Å
NMR ensemble rmsDistance rms dev: 0.0266 Å / Distance rms dev error: 0.0018 Å

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