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- PDB-1jye: Structure of a Dimeric Lac Repressor with C-terminal Deletion and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jye | ||||||
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Title | Structure of a Dimeric Lac Repressor with C-terminal Deletion and K84L Substitution | ||||||
![]() | 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 | ![]() | 70 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.6 KB | Display | ![]() |
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Full document | ![]() | 384.2 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 11.3 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: 37426.691 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DELETION MUTANT / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE DIFFERENCE AT POSITION 109 IS A DIFFERENCE IN THE SEQUENCE REPORTED BY FARABAUGH, P.J. (1978) ...THE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % | |||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Sodium Acetate, Sodium Citrate, 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: BRANDEIS - B4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→17 Å / Num. obs: 44403 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.8 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.5 |
Reflection shell | Highest resolution: 1.7 Å / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 7.2 / % possible all: 72.7 |
Reflection | *PLUS Num. measured all: 258845 |
Reflection shell | *PLUS % possible obs: 72.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: lac repressor Resolution: 1.7→9.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1304025.4 / Data cutoff high rms absF: 1304025.4 / 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: 66.1617 Å2 / ksol: 0.520559 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→9.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / 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 % / Rfactor obs: 0.223 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.284 |