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- PDB-5ipa: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ipa | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with (E)-3-(furan-3-yl)-1-(pyrrolidin-1-yl)prop-2-en-1-one at 1.78A resolution | ||||||||||||
![]() | TetR-family transcriptional regulatory repressor protein | ||||||||||||
![]() | TRANSCRIPTION / EthR / represor / boosting effect | ||||||||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Blaszczyk, M. / Surade, S. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Fragment-Sized EthR Inhibitors Exhibit Exceptionally Strong Ethionamide Boosting Effect in Whole-Cell Mycobacterium tuberculosis Assays. Authors: Nikiforov, P.O. / Blaszczyk, M. / Surade, S. / Boshoff, H.I. / Sajid, A. / Delorme, V. / Deboosere, N. / Brodin, P. / Baulard, A.R. / Barry, C.E. / Blundell, T.L. / Abell, C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 439.3 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ioyC ![]() 5iozC ![]() 5ip6C ![]() 5j1rC ![]() 5j1uC ![]() 5j1yC ![]() 5j3lC ![]() 1t56S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 23781.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ethR, MRA_3895 / Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulphate, Glycerol, MES / PH range: 6.3 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.73→86.63 Å / Num. obs: 53926 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Net I/σ(I): 17 / Num. measured all: 346609 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T56 Resolution: 1.78→26.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.687 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.095 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.46 Å2 / Biso mean: 25.421 Å2 / Biso min: 10.57 Å2
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Refinement step | Cycle: final / Resolution: 1.78→26.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.776→1.821 Å / Total num. of bins used: 20
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