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- PDB-3g1m: EthR from Mycobacterium tuberculosis in complex with compound BDM31381 -

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Entry
Database: PDB / ID: 3g1m
TitleEthR from Mycobacterium tuberculosis in complex with compound BDM31381
ComponentsTRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
KeywordsTRANSCRIPTION / TetR Family / DNA-binding / Transcription regulation
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 / regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / Transcriptional regulator EthR, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily ...: / Transcriptional regulator EthR, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-RF3 / HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsWilland, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. ...Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. / Delcroix, G. / Frenois, F. / Aumercier, M. / Locht, C. / Villeret, V. / Deprez, B. / Baulard, A.R.
Citation
Journal: Nat.Med. (N.Y.) / Year: 2009
Title: Synthetic EthR inhibitors boost antituberculous activity of ethionamide.
Authors: Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. / Delcroix, G. / Frenois, F. / Aumercier, M. / ...Authors: Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. / Delcroix, G. / Frenois, F. / Aumercier, M. / Locht, C. / Villeret, V. / Deprez, B. / Baulard, A.R.
#1: Journal: Tuberculosis / Year: 2006
Title: Insights into mechanisms of induction and ligands recognition in the transcriptional repressor EthR from Mycobacterium tuberculosis.
Authors: Frenois, F. / Baulard, A.R. / Villeret, V.
#2: Journal: Mol.Cell / Year: 2004
Title: Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis.
Authors: Frenois, F. / Engohang-Ndong, J. / Locht, C. / Baulard, A.R. / Villeret, V.
#3: Journal: Mol.Microbiol. / Year: 2004
Title: EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator.
Authors: Engohang-Ndong, J. / Baillat, D. / Aumercier, M. / Bellefontaine, F. / Besra, G.S. / Locht, C. / Baulard, A.R.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3132
Polymers25,9531
Non-polymers3591
Water4,918273
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A: TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
hetero molecules

A: TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6254
Polymers51,9062
Non-polymers7192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3070 Å2
ΔGint-21 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.870, 121.870, 33.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

21A-350-

HOH

31A-356-

HOH

41A-391-

HOH

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR / Transcriptional regulator / TetR family


Mass: 25953.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ethR, MT3970, Rv3855 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96222, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-RF3 / 1-(thiophen-2-ylacetyl)-4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine


Mass: 359.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17 M ammonium sulfate, 0.085 M Na-cacodylate (pH 6.5), 15% glycerol, and 25% polyethylene glycol 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→5 Å / Num. all: 25928 / Num. obs: 25928 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.739 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.754 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21269 1377 5 %RANDOM
Rwork0.18164 ---
obs0.18318 25928 100 %-
all-25928 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 24 273 1807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221569
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9652140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7595193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10223.78474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14715242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021215
X-RAY DIFFRACTIONr_nbd_refined0.2060.2889
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.247
X-RAY DIFFRACTIONr_mcbond_it0.9521.5992
X-RAY DIFFRACTIONr_mcangle_it1.49721556
X-RAY DIFFRACTIONr_scbond_it2.363651
X-RAY DIFFRACTIONr_scangle_it3.64.5584
LS refinement shellResolution: 1.7→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 87 -
Rwork0.27 1754 -
obs--100 %

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