[English] 日本語
Yorodumi- PDB-5j1y: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j1y | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with 1-(pyrrolidin-1-yl)-3-(tetrahydrofuran-3-yl)propan-1-one at 1.81A resolution | ||||||||||||
Components | EthR | ||||||||||||
Keywords | TRANSCRIPTION / EthR / represor / boosting effect | ||||||||||||
Function / homology | Function and homology information monooxygenase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||||||||
Authors | Blaszczyk, M. / Surade, S. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | United Kingdom, United States, 3items
| ||||||||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5j1y.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5j1y.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 5j1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j1y_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5j1y_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 5j1y_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 5j1y_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j1y ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j1y | HTTPS FTP |
-Related structure data
Related structure data | 5ioyC 5iozC 5ip6C 5ipaC 5j1rC 5j1uC 5j3lC 1t56S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 23781.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: ethR_2, ethR, ethR_1, AFL40_4013, BN1213_00375, BN1303_02839, ERS007657_00006, ERS007665_03402, ERS007670_00101, ERS007672_00126, ERS007679_01009, ERS007681_01169, ERS007688_00760, ERS007703_ ...Gene: ethR_2, ethR, ethR_1, AFL40_4013, BN1213_00375, BN1303_02839, ERS007657_00006, ERS007665_03402, ERS007670_00101, ERS007672_00126, ERS007679_01009, ERS007681_01169, ERS007688_00760, ERS007703_00420, ERS007722_01164, ERS007741_02569, ERS013447_02283, ERS013471_02551, ERS023446_02032, ERS024213_01441, ERS024276_01130, ERS027644_00684, ERS027646_02322, ERS027654_00374, ERS027656_00876, ERS031537_01716, ERS075357_02728, ERS075361_00362, ERS075387_01097, ERS124361_02860, IQ38_20160, IQ40_19545, IQ45_19480, IQ47_19420, IU13_19735, IU16_19625 Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KCS8, UniProt: P9WMC1*PLUS | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.78 % |
---|---|
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 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.983 Å | |||||||||||||||
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: 1.79→85.9 Å / Num. obs: 48182 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Net I/σ(I): 11.7 / Num. measured all: 308594 | |||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T56 Resolution: 1.81→29.45 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.348 / SU ML: 0.072 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.123 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.94 Å2 / Biso mean: 19.276 Å2 / Biso min: 3.46 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.81→29.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
|