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- PDB-3zqi: Structure of Tetracycline repressor in complex with inducer pepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zqi | ||||||
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Title | Structure of Tetracycline repressor in complex with inducer peptide- TIP2 | ||||||
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![]() | TRANSCRIPTION / TETR / PEPTIDIC EFFECTORS / ALLOSTERY | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sevvana, M. / Goeke, D. / Stoeckle, C. / Kaspar, D. / Grubmueller, S. / Goetz, C. / Wimmer, C. / Berens, C. / Klotzsche, M. / Muller, Y.A. / Hillen, W. | ||||||
![]() | ![]() Title: An Exclusive Alpha/Beta Code Directs Allostery in Tetr-Peptide Complexes. Authors: Sevvana, M. / Goetz, C. / Goeke, D. / Wimmer, C. / Berens, C. / Hillen, W. / Muller, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.3 KB | Display | ![]() |
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PDB format | ![]() | 156.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.9 KB | Display | ![]() |
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Full document | ![]() | 501.2 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zqfC ![]() 3zqgC ![]() 3zqhC ![]() 2ns8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 23531.662 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-187,188-208 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CHIMERIC PROTEIN, RESIDUES 1-187 ARE FROM VARIANT B, RESIDUES 188-208 ARE FROM VARIANT D COMPND Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2034.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 452 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 68 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 88 TO ASN ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 7.0, 20% PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-225 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 71948 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 7.28 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.07 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 7.18 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.74 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NS8 Resolution: 1.5→24.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.127 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→24.88 Å
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Refine LS restraints |
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