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- PDB-1jyf: Structure of the Dimeric Lac Repressor with an 11-residue C-termi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jyf | ||||||
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Title | Structure of the Dimeric Lac Repressor with an 11-residue C-terminal Deletion. | ||||||
![]() | Lactose Operon Repressor | ||||||
![]() | TRANSCRIPTION / Gene Regulation / Protein Stability / Protein DNA-binding | ||||||
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 | ![]() ![]() | ||||||
![]() | Bell, C.E. / Barry, J. / Matthews, K.S. / Lewis, M. | ||||||
![]() | ![]() Title: Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator. Authors: Bell, C.E. / Barry, J. / Matthews, K.S. / Lewis, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379 KB | Display | ![]() |
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Full document | ![]() | 385.2 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37442.715 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DELETION Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.56 % | |||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Sodium Citrate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||
Crystal | *PLUS Density % sol: 50 % | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→45.6 Å / Num. obs: 9811 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.5 |
Reflection shell | Highest resolution: 3 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.5 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 64464 |
Reflection shell | *PLUS % possible obs: 99.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Lac repressor dimer Resolution: 3→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2855017.57 / Data cutoff high rms absF: 2855017.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.301 Å2 / ksol: 0.339368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.313 |