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Yorodumi- PDB-2kej: Solution structure of a dimer of LAC repressor DNA-binding domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kej | ||||||
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Title | Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O2 | ||||||
Components |
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Keywords | Transcription/DNA / Lac repressor / lac operators / protein-DNA complex / DNA-binding / Repressor / Transcription / Transcription regulation / Transcription-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Romanuka, J. / Folkers, G. / Biris, N. / Tishchenko, E. / Wienk, H. / Kaptein, R. / Boelens, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. Authors: Romanuka, J. / Folkers, G.E. / Biris, N. / Tishchenko, E. / Wienk, H. / Bonvin, A.M. / Kaptein, R. / Boelens, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kej.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kej.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2kej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kej_validation.pdf.gz | 372.1 KB | Display | wwPDB validaton report |
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Full document | 2kej_full_validation.pdf.gz | 804.5 KB | Display | |
Data in XML | 2kej_validation.xml.gz | 59.6 KB | Display | |
Data in CIF | 2kej_validation.cif.gz | 88.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/2kej ftp://data.pdbj.org/pub/pdb/validation_reports/ke/2kej | HTTPS FTP |
-Related 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: 6822.755 Da / Num. of mol.: 2 / Fragment: UNP residues 1-62 / Mutation: V52C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: lacI, b0345, JW0336 / Production host: Escherichia coli (E. coli) / Strain (production host): DH9 / References: UniProt: P03023 #2: DNA chain | | Mass: 7147.650 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 6973.493 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.7 mM DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DGP*DAP*DTP*DAP*DAP*DCP*DAP*DAP*DTP*DTP*DT)'), 0.7 mM DNA (5'- ...Contents: 0.7 mM DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DGP*DAP*DTP*DAP*DAP*DCP*DAP*DAP*DTP*DTP*DT)'), 0.7 mM DNA (5'-D(P*DAP*DAP*DAP*DTP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DTP*DC)'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.03 / pH: 6 / Pressure: ambient / Temperature: 315 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |