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Yorodumi- PDB-8ke8: Crystal structure of TetR-type transcriptional factor NalC from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ke8 | ||||||
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Title | Crystal structure of TetR-type transcriptional factor NalC from P. aeruginosa | ||||||
Components | NalC | ||||||
Keywords | DNA BINDING PROTEIN / NalC / TetR-type transcriptional factor / Multi-drug efflux system | ||||||
Function / homology | Function and homology information negative regulation of transmembrane transport / negative regulation of transporter activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Lee, J.Y. / Jeong, K.H. / Ko, J.H. / Son, S.B. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Structural insights into the transcriptional regulator NalC, a key component of the MexAB-OprM efflux pump system, from Pseudomonas aeruginosa. Authors: Jeong, K.H. / Ko, J.H. / Son, S.B. / Lee, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ke8.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ke8.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ke8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ke8_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 8ke8_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 8ke8_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 8ke8_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/8ke8 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/8ke8 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23558.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: nalC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9HXS0 #2: 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: 2.44 Å3/Da / Density % sol: 49.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 0.2 M Ammonium chloride, 0.1 M MES pH 6.25, 1.0 M Potassium sodium tartrate |
-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: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 26116 / % possible obs: 99.8 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 34.52 |
Reflection shell | Resolution: 2.05→2.09 Å / Rmerge(I) obs: 0.361 / Num. unique obs: 1257 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold Resolution: 2.05→19.67 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.16 / Stereochemistry target values: ML
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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: 2.05→19.67 Å
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Refine LS restraints |
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LS refinement shell |
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