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Yorodumi- PDB-6l33: Crystal structure of the regulatory domain of MexT, a transcripti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l33 | ||||||
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Title | Crystal structure of the regulatory domain of MexT, a transcriptional activator in Pseudomonas aeruginosa | ||||||
Components | MexT protein | ||||||
Keywords | TRANSCRIPTION / LysR-type transcriptional regulator / antibiotic resistance / regulatory domain | ||||||
Function / homology | Function and homology information negative regulation of secondary metabolite biosynthetic process / DNA-binding transcription activator activity / negative regulation of protein secretion / negative regulation of proteolysis / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Kim, S. / Ha, N.-C. | ||||||
Citation | Journal: Mol.Cells / Year: 2019 Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEFOprN Efflux Pump inPseudomonas aeruginosa. Authors: Kim, S. / Kim, S.H. / Ahn, J. / Jo, I. / Lee, Z.W. / Choi, S.H. / Ha, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l33.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l33.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 6l33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l33_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6l33_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6l33_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 6l33_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/6l33 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/6l33 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: Protein | Mass: 23193.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O87785, UniProt: Q9I0Z0*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.5 M Ammonium sulfate, 0.1 M lithium sulfate, 1.0 M sodium citrate tribasic dehydrate (pH 5.6), 2 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 53533 / % possible obs: 97.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 22.18 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 23.76 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 2444 / CC1/2: 0.633 / Rpim(I) all: 0.19 / Rrim(I) all: 0.4 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→31.84 Å / SU ML: 0.2301 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 22.9803 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→31.84 Å
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Refine LS restraints |
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LS refinement shell |
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