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- PDB-1l1m: SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l1m | ||||||
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Title | SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1 | ||||||
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![]() | TRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATION / LAC OPERON / LAC REPRESSOR / NATURAL LAC OPERATOR / ASYMMETRIC DNA-BINDING / HTH / TRANSCRIPTION REGULATOR-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MDR | ||||||
![]() | Kalodimos, C.G. / Bonvin, A.M.J.J. / Salinas, R.K. / Wechselberger, R. / Boelens, R. / Kaptein, R. | ||||||
![]() | ![]() Title: Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. Authors: Kalodimos, C.G. / Bonvin, A.M. / Salinas, R.K. / Wechselberger, R. / Boelens, R. / Kaptein, R. #1: ![]() Title: Strong DNA binding by covalently linked dimeric lac headpiece: evidence for the crucial role of the hinge helices Authors: Kalodimos, C.G. / Folkers, G. / Boelens, R. / Kaptein, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 377.8 KB | Display | ![]() |
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Full document | ![]() | 847.7 KB | Display | |
Data in XML | ![]() | 69.8 KB | Display | |
Data in CIF | ![]() | 98.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 7143.645 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Lac operator O1; this is the wild-type operator sequence of the lac operon in E. coli. |
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#2: DNA chain | Mass: 6974.534 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Lac operator O1; this is the wild-type operator sequence of the lac operon in E. coli. |
#3: Protein | Mass: 6822.755 Da / Num. of mol.: 2 / Fragment: N-terminal DNA-binding domain, Residues 1-62 / Mutation: V52C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D and 3D homo- and heteronuclearnuclear techniques. 13C-15N labeled protein was used and unlabeled nucleotide. IN ADDITION ISOTOPE FILTER ...Text: This structure was determined using standard 2D and 3D homo- and heteronuclearnuclear techniques. 13C-15N labeled protein was used and unlabeled nucleotide. IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO OBTAIN ADDITIONAL ASSIGNMENTS AND TO ASSIGN INTER-MOLECULAR NOES. FOR FURTHER DETAILS SEE THE REFERENCE DESCRIBING THE STRUCTURES. |
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Sample preparation
Details | Contents: 2mM Lac-HP62-V52C U-15N,13C, 10mM KPi, 20mM KCl, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 10mM KPi, 20mM KCl / pH: 6.0 / Pressure: ambient / Temperature: 315 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 |
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Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, RESTRAINED MDR / Software ordinal: 1 Details: The structure of the complex was calculated as follows. First the structure of the dimeric lac HP62-V52C was calculated using only protein NMR restraints. The 50 best structures were ...Details: The structure of the complex was calculated as follows. First the structure of the dimeric lac HP62-V52C was calculated using only protein NMR restraints. The 50 best structures were selected and docked onto the natural lac operator B-DNA using simulated annealing. Distance and planarity restraints for the DNA were incorporated in order to keep DNA close to B-DNA but allowing a bend necessary to accommodate the two headpiece molecules on the DNA. | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |