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Open data
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Basic information
Entry | Database: PDB / ID: 1jwl | |||||||||
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Title | Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex | |||||||||
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![]() | TRANSCRIPTION/DNA / Lac Repressor / Gene Regulation / DNA-Bending / TRANSCRIPTION-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 | ![]() ![]() | |||||||||
![]() | Bell, C.E. / Lewis, M. | |||||||||
![]() | ![]() Title: Crystallographic analysis of Lac repressor bound to natural operator O1. Authors: Bell, C.E. / Lewis, M. | |||||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 CHAIN(S). BIOMOLECULE 1 IS COMPLETE BUT BIOMOLECULE 2 IS INCOMPLETE. BIOMOLECULE 2 DOES NOT CONTAIN THE DNA CHAINS BECAUSE THEY ARE DISORDERED. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197 KB | Display | ![]() |
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PDB format | ![]() | 152 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 579.3 KB | Display | ![]() |
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Full document | ![]() | 610.9 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1efaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 7152.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: O1 top strand | ||
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#2: DNA chain | Mass: 6965.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: O1 bottom strand | ||
#3: Protein | Mass: 35756.797 Da / Num. of mol.: 3 / Fragment: C-terminal deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Sugar | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.36 Å3/Da / Density % sol: 77.06 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 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: 4→16 Å / Num. all: 68073 / Num. obs: 20847 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.111 / Net I/σ(I): 7.9 |
Reflection shell | Highest resolution: 4 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.277 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 68073 / Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS % possible obs: 93.9 % / Rmerge(I) obs: 0.277 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EFA Resolution: 4→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 128004.13 / 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: 64.8743 Å2 / ksol: 0.361311 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.23 Å / Rfactor Rfree error: 0.016 / 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: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 67.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.291 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.272 |