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Yorodumi- PDB-2fj1: Crystal Structure Analysis of Tet Repressor (class D) in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fj1 | ||||||
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Title | Crystal Structure Analysis of Tet Repressor (class D) in Complex with 7-Chlortetracycline-Nickel(II) | ||||||
Components | Tetracycline repressor protein class D | ||||||
Keywords | TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION / helix-turn-helix / metal coordination | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Orth, P. / Saenger, W. / Palm, G.J. / Hinrichs, W. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2008 Title: Specific binding of divalent metal ions to tetracycline and to the Tet repressor/tetracycline complex. Authors: Palm, G.J. / Lederer, T. / Orth, P. / Saenger, W. / Takahashi, M. / Hillen, W. / Hinrichs, W. #1: Journal: Science / Year: 1994 Title: Structure of the TET repressor-tetracycline complex and regulation of antibiotic resistance Authors: Hinrichs, W. / Kisker, C. / Duevel, M. / Mueller, A. / Tovar, K. / Hillen, W. / Saenger, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fj1.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fj1.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 2fj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fj1_validation.pdf.gz | 859.2 KB | Display | wwPDB validaton report |
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Full document | 2fj1_full_validation.pdf.gz | 865.5 KB | Display | |
Data in XML | 2fj1_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 2fj1_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/2fj1 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/2fj1 | HTTPS FTP |
-Related structure data
Related structure data | 2vkeC 2tctS 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: 23288.334 Da / Num. of mol.: 1 / Fragment: residues 2-208 / Mutation: A2S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Plasmid: PWH610 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 DELTA H1 DELTA TRP / References: UniProt: P0ACT4 | ||||
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#2: Chemical | ChemComp-NI / | ||||
#3: Chemical | #4: Chemical | ChemComp-CTC / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.58 M Ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 1997 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→64.5 Å / Num. all: 10706 / Num. obs: 10706 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 32.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.2→2.258 Å / Mean I/σ(I) obs: 3.2 / Num. unique all: 751 / Rsym value: 0.268 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TCT Resolution: 2.2→64.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.467 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.999 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→64.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.258 Å / Total num. of bins used: 20 /
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