+Open data
-Basic information
Entry | Database: PDB / ID: 4d7m | |||||||||
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Title | TetR(D) in complex with anhydrotetracycline and magnesium | |||||||||
Components | TETRACYCLINE REPRESSOR PROTEIN CLASS D | |||||||||
Keywords | TRANSCRIPTION / ANTIBIOTIC RESISTANCE / TETR | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Werten, S. / Dalm, D. / Palm, G.J. / Hinrichs, W. | |||||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Tetracycline Repressor Allostery Does not Depend on Divalent Metal Recognition. Authors: Werten, S. / Dalm, D. / Palm, G.J. / Grimm, C.C. / Hinrichs, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d7m.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d7m.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 4d7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7m ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7m | HTTPS FTP |
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-Related structure data
Related structure data | 2xpuC 4d7nC 4v2fC 4v2gC 2trtS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24333.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH208 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: P0ACT4 |
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-Non-polymers , 5 types, 186 molecules
#2: Chemical | ChemComp-TDC / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.6 % / Description: NONE |
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Crystal grow | pH: 9 Details: 50 MM TRIS-HCL PH 9.0, 1 M (NH4)2SO4, 70 MM NACL, 10 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Date: May 1, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→28.9 Å / Num. obs: 28546 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2.94 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TRT Resolution: 1.55→61.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.394 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / 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: 29.096 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→61.6 Å
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Refine LS restraints |
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