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Yorodumi- PDB-6dm7: NMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGG) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dm7 | ||||||
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Title | NMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGG) | ||||||
Components |
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Keywords | DNA / Sp1 Consensus Sequence | ||||||
Function / homology | DNA Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Davis, E.V. / Hennig, M. / Arya, D.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences Authors: Davis, E.V. / Hennig, M. / Arya, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dm7.cif.gz | 220.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dm7.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 6dm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dm7_validation.pdf.gz | 341.6 KB | Display | wwPDB validaton report |
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Full document | 6dm7_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 6dm7_validation.xml.gz | 7 KB | Display | |
Data in CIF | 6dm7_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/6dm7 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/6dm7 | HTTPS FTP |
-Related structure data
Related structure data | 6dvtC 6dxmC 6ed9C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 2877.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Watson-Crick DNA duplex chain A / Source: (synth.) Homo sapiens (human) |
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#2: DNA chain | Mass: 2597.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Watson-Crick DNA duplex chain B / Source: (synth.) Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Details: equal molar eq. d(GGGGCGGGG).d(CCCCGCCCC) 100% D2O 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0 Ionic strength: 30 mM Na+ mM / Label: non-exchange / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: 214 NOE distance constraints, 54 hydrogen distance restraints, 48 dihedral angle restraints. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 20 |