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Yorodumi- PDB-2xgd: Crystal structure of a designed homodimeric variant T-A(L)A(L) of... -
+Open data
-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 | ||||||
Components | TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D | ||||||
Keywords | TRANSCRIPTION / CHIMERA / TRANSCRIPTION REGULATION / ANTIBIOTIC RESISTANCE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 | 2xgd.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xgd.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xgd_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 2xgd_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 2xgd_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2xgd_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xgd ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xgd | HTTPS FTP |
-Related structure data
Related structure data | 2xgcC 2xgeC 1a6iS 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: 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.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04483, UniProt: P0ACT4 | ||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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