+Open data
-Basic information
Entry | Database: PDB / ID: 1lwa | ||||||
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Title | Solution Structure of SRY_DNA | ||||||
Components |
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Keywords | DNA / double-stranded dna | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing relaxation matrix | ||||||
Authors | Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lwa.cif.gz | 369.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lwa.ent.gz | 318.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lwa ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lwa | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | 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. |
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#2: DNA chain | 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. |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2.2 mM DNA / Solvent system: 90% H2O, 10% D2O or 100% D2O |
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Sample conditions | Ionic strength: low NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 100 / Conformers submitted total number: 20 |