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Yorodumi- PDB-6nsn: TetR family transcriptional regulator CifR C99T-C181R Cysteines m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nsn | ||||||||||||
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Title | TetR family transcriptional regulator CifR C99T-C181R Cysteines mutant complexed with 26bp double-strand operator DNA | ||||||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Repressor / DNA-binding complex / Epoxide sensing / TRANSCRIPTION-DNA complex | ||||||||||||
Function / homology | Function and homology information regulation of biosynthetic process / regulation of primary metabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | He, S. / Madden, D.R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biorxiv / Year: 2024 Title: Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa Authors: He, S. / Taher, N.M. / Hvorecny, K.L. / Ragusa, M.J. / Bahl, C.D. / Hickman, A.B. / Dyda, F. / Madden, D.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nsn.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nsn.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 6nsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nsn_validation.pdf.gz | 450 KB | Display | wwPDB validaton report |
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Full document | 6nsn_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 6nsn_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6nsn_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/6nsn ftp://data.pdbj.org/pub/pdb/validation_reports/ns/6nsn | HTTPS FTP |
-Related structure data
Related structure data | 6nsmC 6nsrSC 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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Unit cell |
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-Components
#1: Protein | Mass: 21989.965 Da / Num. of mol.: 2 / Mutation: C99T,C181R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: PA14_26140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZCS5, UniProt: Q9HZR6*PLUS #2: DNA chain | | Mass: 7941.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) #3: DNA chain | | Mass: 8026.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) #4: 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: 3.75 Å3/Da / Density % sol: 67.2 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris, pH 7.5, 0.2 M magnesium chloride, 16% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979075 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979075 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.861 Å / Num. obs: 28028 / % possible obs: 99.89 % / Redundancy: 12.2 % / Biso Wilson estimate: 66.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.111 / Net I/σ(I): 17.41 |
Reflection shell | Resolution: 2.6→2.6929 Å / Num. unique obs: 2961 / CC1/2: 0.723 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6NSR Resolution: 2.6→29.861 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.861 Å
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Refine LS restraints |
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LS refinement shell |
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