+Open data
-Basic information
Entry | Database: PDB / ID: 1e7j | ||||||
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Title | HMG-D complexed to a bulge DNA | ||||||
Components |
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Keywords | PROTEIN/DNA / PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information Mitochondrial transcription initiation / Mitochondrial protein degradation / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / chromatin organization / transcription cis-regulatory region binding / chromatin / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, MINIMIZATION | ||||||
Authors | Cerdan, R. / Payet, D. / Yang, J.-C. / Travers, A.A. / Neuhaus, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Hmg-D Complexed to a Bulge DNA: An NMR Model Authors: Cerdan, R. / Payet, D. / Yang, J.-C. / Travers, A.A. / Neuhaus, D. #1: Journal: Structure / Year: 1994 Title: The Solution Structure and Dynamics of the DNA-Binding Domain of Hmg-D from Drosophila Melanogaster Authors: Jones, D.N.M. / Searles, M.A. / Shaw, G.L. / Churchill, M.E.A. / Ner, S.S. / Keeler, J. / Travers, A.A. / Neuhaus, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e7j.cif.gz | Display | PDBx/mmCIF format | |
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PDB format | pdb1e7j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 1e7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/1e7j ftp://data.pdbj.org/pub/pdb/validation_reports/e7/1e7j | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8501.711 Da / Num. of mol.: 1 / Fragment: HMG-D DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET13A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05783 |
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#2: DNA chain | Mass: 4288.817 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | Ionic strength: LOW / pH: 6 / Temperature: 293 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, MINIMIZATION / Software ordinal: 1 / Details: REFINEMENT DETAILS WILL BE FOUND IN THE PAPER | ||||||||||||||||
NMR ensemble | Conformer selection criteria: LOW VALUES OF THE NOE ENERGY TERM AND PROTEIN LOCATED WITHIN MINOR GROOVE OF DNA Conformers calculated total number: 50 / Conformers submitted total number: 10 |