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- PDB-2xge: Crystal structure of a designed heterodimeric variant T-A(A)B of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xge | ||||||
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Title | Crystal structure of a designed heterodimeric variant T-A(A)B of the tetracycline repressor | ||||||
![]() | (TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS ...) x 2 | ||||||
![]() | 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 | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xgcC ![]() 2xgdC ![]() 1a6iS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS ... , 2 types, 2 molecules AB
#1: Protein | Mass: 23444.643 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-50,51-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 23710.916 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-50,51-208 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 109 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 136 TO TRP ENGINEERED RESIDUE IN CHAIN B, PHE 140 TO ALA ...ENGINEERED |
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Sequence details | ENGINEERED VARIANT, NAMELY CHIMERA OF P04483 AND P0ACT4 ( UNIPROT ACCESSION NUMBERS) AUTHOR HAS ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→2.23 Å / Num. obs: 13364 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 5.6 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A6I Resolution: 2.14→19.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.919 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.218 / 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. THE CRYSTAL STRUCTURE ...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. THE CRYSTAL STRUCTURE CORRESPONDS TO A HETERODIMER WITH CHAINS A AND B. BOTH CHAINS DIFFER AT ONLY 5 POSITIONS. THE DATA HAS BEEN EXPLAINED A BIMODAL DISORDER MODEL IN WHICH BOTH CHAINS ARE PRESENT WITH 0.5 OCCUPANCY IN THE ASYMMETRIC UNIT AT THE SAME TIME.
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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: 49.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→19.96 Å
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Refine LS restraints |
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