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- PDB-3g1l: EthR from Mycobacterium tuberculosis in complex with compound BDM14744 -

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Entry
Database: PDB / ID: 3g1l
TitleEthR from Mycobacterium tuberculosis in complex with compound BDM14744
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
3-(4-fluorophenyl)-5-phenyl-4H-1,2,4-triazole / 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)28,3642
Polymers28,1241
Non-polymers2391
Water1,964109
1
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)56,7274
Polymers56,2492
Non-polymers4782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2970 Å2
ΔGint-22 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.738, 121.738, 33.669
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-284-

HOH

21A-285-

HOH

31A-286-

HOH

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Components

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


Mass: 28124.447 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(D3) / References: UniProt: P96222, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-RF2 / 3-(4-fluorophenyl)-5-phenyl-4H-1,2,4-triazole


Mass: 239.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10FN3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.17M ammonium sulfate, 0.085M Na-cacodylate (pH 6.5), 15% glycerol, and 25% polyethylene glycol 8000, EVAPORATION, temperature 293K

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Data collection

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→19.47 Å / Num. all: 26494 / Num. obs: 26494 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.744 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CCP4model building
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→19.47 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.867 / SU B: 6.22 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27787 1394 5 %RANDOM
Rwork0.23106 ---
all0.23341 26494 --
obs0.23341 26494 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 18 109 1637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221562
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9612130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9665193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75723.78474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92615242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021212
X-RAY DIFFRACTIONr_nbd_refined0.2080.2785
X-RAY DIFFRACTIONr_nbtor_refined0.30.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.220
X-RAY DIFFRACTIONr_mcbond_it1.3481.5996
X-RAY DIFFRACTIONr_mcangle_it1.90321556
X-RAY DIFFRACTIONr_scbond_it2.6763647
X-RAY DIFFRACTIONr_scangle_it3.724.5574
X-RAY DIFFRACTIONr_rigid_bond_restr1.70931643
X-RAY DIFFRACTIONr_sphericity_free6.6113109
X-RAY DIFFRACTIONr_sphericity_bonded2.79631529
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 101 -
Rwork0.269 1916 -
obs--100 %

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