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- PDB-2xgd: Crystal structure of a designed homodimeric variant T-A(L)A(L) of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xgd | ||||||
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Title | Crystal structure of a designed homodimeric variant T-A(L)A(L) of the tetracycline repressor | ||||||
![]() | TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D | ||||||
![]() | TRANSCRIPTION / CHIMERA / TRANSCRIPTION REGULATION / ANTIBIOTIC RESISTANCE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Stiebritz, M.T. / Wengrzik, S. / Richter, J.P. / Muller, Y.A. | ||||||
![]() | ![]() Title: Computational Design of a Chain-Specific Tetracycline Repressor Heterodimer. Authors: Stiebritz, M.T. / Wengrzik, S. / Klein, D.L. / Richter, J.P. / Srebrzynski, A. / Weiler, S. / 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 | ![]() | 93.7 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.7 KB | Display | ![]() |
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Full document | ![]() | 432.4 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xgcC ![]() 2xgeC ![]() 1a6iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23486.723 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-50,51-208 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | ENGINEERED VARIANT, NAMELY CHIMERA OF P04483 AND P0ACT4 ( UNIPROT ACCESSION NUMBERS) AND 2 ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. obs: 11142 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.25→2.39 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.2 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A6I Resolution: 2.25→34.84 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 17.216 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.629 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→34.84 Å
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Refine LS restraints |
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