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- PDB-1lwa: Solution Structure of SRY_DNA -

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Basic information

Entry
Database: PDB / ID: 1lwa
TitleSolution Structure of SRY_DNA
Components
  • 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'
  • 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'
KeywordsDNA / double-stranded dna
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing relaxation matrix
AuthorsMasse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding
Authors: Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J.
History
DepositionMay 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'
B: 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,1792
Polymers9,1792
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)20 / 100structures with acceptable covalent geometry
RepresentativeModel #15closest to the average

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Components

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


Mass: 4696.042 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Derived from the sequence recognized by the sequence-specific HMGB protein SRY.
#2: DNA chain 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'


Mass: 4482.940 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Derived from the sequence recognized by the sequence-specific HMGB protein SRY.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1116 2D NOESYs (Tmix=25,50,75,100,200,300 ms)
12111 echo NOESY

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Sample preparation

DetailsContents: 2.2 mM DNA / Solvent system: 90% H2O, 10% D2O or 100% D2O
Sample conditionsIonic strength: low NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
Felix2000MSIdata analysis
X-PLOR3.1Brungerstructure solution
XwinNMR3.1Brungeriterative matrix relaxation
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing relaxation matrix / Software ordinal: 1
Details: Structures calculated with a total of 780 experimental restraints. 76 hydrogen bond restraints for Watson-Crick base pairing were also included.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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