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- PDB-8qdh: Engineered LmrR carrying a cyclic boronate ester formed between T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qdh | ||||||
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Title | Engineered LmrR carrying a cyclic boronate ester formed between Tris and p-boronophenylalanine at position 89 | ||||||
![]() | Transcriptional regulator, PadR-like family | ||||||
![]() | TRANSCRIPTION / Artificial enzyme / boron catalysis / unnatural amino acid / 4-boronophenylalanine | ||||||
Function / homology | Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator, PadR-like family![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thunnissen, A.M.W.H. / Rozeboom, H.J. / Longwitz, L. / Leveson-Gower, R.B. / Roelfes, G. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Boron catalysis in a designer enzyme. Authors: Longwitz, L. / Leveson-Gower, R.B. / Rozeboom, H.J. / Thunnissen, A.W.H. / Roelfes, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.7 KB | Display | ![]() |
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PDB format | ![]() | 120 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.4 KB | Display | ![]() |
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Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qdfC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15272.956 Da / Num. of mol.: 2 Mutation: M8H, A92L, F93E, M89 replaced with p-boronophenylalanine Source method: isolated from a genetically manipulated source Details: LmrR carrying a C-terminal strep-tag, with mutations M8H, A92L, F93E and with M89 replaced with para-boronophenylalanine. The para-boronophenylalanine at position 89 has reacted with Tris to ...Details: LmrR carrying a C-terminal strep-tag, with mutations M8H, A92L, F93E and with M89 replaced with para-boronophenylalanine. The para-boronophenylalanine at position 89 has reacted with Tris to form a cyclic boronate ester Source: (gene. exp.) ![]() Gene: llmg_0323 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein was concentrated to 6.5 mg/ml in 20 mM Tris-HCl, pH 8.0, 280 mM NaCl and 1 mM EDTA. Reservoir solution contained 0.2 M NaCl, 20% PEG 6000 in 0.1 M MES, pH 6.0. Crystal was cryo- ...Details: Protein was concentrated to 6.5 mg/ml in 20 mM Tris-HCl, pH 8.0, 280 mM NaCl and 1 mM EDTA. Reservoir solution contained 0.2 M NaCl, 20% PEG 6000 in 0.1 M MES, pH 6.0. Crystal was cryo-protected by addition of 25% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→49.49 Å / Num. obs: 25538 / % possible obs: 98.2 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Χ2: 0.93 / Net I/σ(I): 14.8 / Num. measured all: 329575 |
Reflection shell | Resolution: 1.72→1.75 Å / % possible obs: 97.6 % / Redundancy: 13.2 % / Rmerge(I) obs: 2.034 / Num. measured all: 17356 / Num. unique obs: 1311 / CC1/2: 0.628 / Rpim(I) all: 0.576 / Rrim(I) all: 2.116 / Χ2: 0.8 / Net I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→47.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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