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Yorodumi- PDB-6rxb: Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rxb | ||||||
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Title | Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with minocycline | ||||||
Components | (Tetracycline repressor protein class ...) x 2 | ||||||
Keywords | TRANSCRIPTION / Transcription regulation | ||||||
Function / homology | Function and homology information response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Tam, H.K. / Himpich, S. / Pos, K.M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Front Microbiol / Year: 2021 Title: Binding of Tetracyclines to Acinetobacter baumannii TetR Involves Two Arginines as Specificity Determinants Authors: Sumyk, M. / Himpich, S. / Foong, W.E. / Herrmann, A. / Pos, K.M. / Tam, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rxb.cif.gz | 314.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxb.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rxb_validation.pdf.gz | 590.4 KB | Display | wwPDB validaton report |
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Full document | 6rxb_full_validation.pdf.gz | 596.6 KB | Display | |
Data in XML | 6rxb_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 6rxb_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxb ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxb | HTTPS FTP |
-Related structure data
Related structure data | 6rx9SC S: Starting model for refinement C: citing same article (ref.) |
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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
-Tetracycline repressor protein class ... , 2 types, 4 molecules BDAC
#1: Protein | Mass: 24246.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain AYE) (bacteria) Strain: AYE / Gene: tetR, ABAYE3639 / Variant: AYE / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CE43 / References: UniProt: B0VCI2 #2: Protein | Mass: 24166.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain AYE) (bacteria) Strain: AYE / Gene: tetR, ABAYE3639 / Variant: AYE / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CE43 / References: UniProt: B0VCI2 |
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-Non-polymers , 6 types, 140 molecules
#3: Chemical | ChemComp-MIY / ( #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-SIN / | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 5.5 Details: 0.1M Sodium cacodylate, pH5.5, 11% PEG Smear Broad, 3% Tacsimate, pH7.0, and 10% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.41 Å / Num. obs: 43315 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.072 / Rrim(I) all: 0.267 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 14 % / Num. unique obs: 3920 / CC1/2: 0.652 / Rpim(I) all: 0.548 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RX9 Resolution: 2.25→48.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 17.695 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.613 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→48.41 Å
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Refine LS restraints |
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