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- PDB-5ip6: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ip6 | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with N-((tetrahydrofuran-3-yl)methyl)pyrrolidine-1-carboxamide at 1.93A 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 | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 36.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 443.2 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ioyC ![]() 5iozC ![]() 5ipaC ![]() 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 | ChemComp-6C9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.47 % |
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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: 1.91→85.73 Å / Num. obs: 39652 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Net I/σ(I): 14.7 / Num. measured all: 252285 | |||||||||||||||
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: 1.93→29.45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.143 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1485 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.136 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: 92.34 Å2 / Biso mean: 28.807 Å2 / Biso min: 9.95 Å2
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Refinement step | Cycle: final / Resolution: 1.93→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.928→1.978 Å / Total num. of bins used: 20
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