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Yorodumi- PDB-2xge: Crystal structure of a designed heterodimeric variant T-A(A)B of ... -
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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 | ||||||
Components | (TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS ...) x 2 | ||||||
Keywords | TRANSCRIPTION / CHIMERA / TRANSCRIPTION REGULATION / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Stiebritz, M.T. / Wengrzik, S. / Richter, J.P. / Muller, Y.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xge.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xge.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xge ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xge | HTTPS FTP |
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-Related structure data
Related structure data | 2xgcC 2xgdC 1a6iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04483, UniProt: P0ACT4 |
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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.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04483, UniProt: P0ACT4 |
-Non-polymers , 4 types, 109 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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