+Open data
-Basic information
Entry | Database: PDB / ID: 1jwl | |||||||||
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Title | Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex | |||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Lac Repressor / Gene Regulation / DNA-Bending / 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 | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4 Å | |||||||||
Authors | Bell, C.E. / Lewis, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 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). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jwl.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jwl.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 1jwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jwl ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jwl | HTTPS FTP |
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-Related structure data
Related structure data | 1efaS S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Escherichia coli (E. coli) / Gene: LacI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03023 #4: Sugar | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |