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- PDB-3qpl: G106W mutant of EthR from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3qpl
TitleG106W mutant of EthR from Mycobacterium tuberculosis
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / HTH motif / transcriptional repressor
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 ...: / 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
HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCarette, X. / Willery, E. / Hoos, S. / Lecat-Guillet, N. / Frenois, F. / Dirie, B. / Villeret, V. / England, P. / Deprez, B. / Locht, C. ...Carette, X. / Willery, E. / Hoos, S. / Lecat-Guillet, N. / Frenois, F. / Dirie, B. / Villeret, V. / England, P. / Deprez, B. / Locht, C. / Willand, N. / Baulard, A.
Citation
Journal: Nucleic Acids Res. / Year: 2012
Title: Structural activation of the transcriptional repressor EthR from Mycobacterium tuberculosis by single amino acid change mimicking natural and synthetic ligands.
Authors: Carette, X. / Blondiaux, N. / Willery, E. / Hoos, S. / Lecat-Guillet, N. / Lens, Z. / Wohlkonig, A. / Wintjens, R. / Soror, S.H. / Frenois, F. / Dirie, B. / Villeret, V. / England, P. / ...Authors: Carette, X. / Blondiaux, N. / Willery, E. / Hoos, S. / Lecat-Guillet, N. / Lens, Z. / Wohlkonig, A. / Wintjens, R. / Soror, S.H. / Frenois, F. / Dirie, B. / Villeret, V. / England, P. / Lippens, G. / Deprez, B. / Locht, C. / Willand, N. / Baulard, A.R.
#1: 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.
#2: Journal: Acs Chem.Biol. / Year: 2010
Title: Exploring Drug Target Flexibility Using in Situ Click Chemistry: Application to a Mycobacterial Transcriptional Regulator.
Authors: Willand, N. / Desroses, M. / Toto, P. / Dirie, B. / Lens, Z. / Villeret, V. / Rucktooa, P. / Locht, C. / Baulard, A. / Deprez, B.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator EthR


Theoretical massNumber of molelcules
Total (without water)26,0821
Polymers26,0821
Non-polymers00
Water00
1
A: HTH-type transcriptional regulator EthR

A: HTH-type transcriptional regulator EthR


Theoretical massNumber of molelcules
Total (without water)52,1642
Polymers52,1642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3060 Å2
ΔGint-23 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.740, 119.740, 33.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HTH-type transcriptional regulator EthR


Mass: 26082.232 Da / Num. of mol.: 1 / Mutation: G106W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, etaR, MT3970, Rv3855 / Production host: Escherichia coli (E. coli) / References: UniProt: P96222, UniProt: P9WMC1*PLUS

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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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: glycerol, polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.18→19 Å / Num. all: 29488 / Num. obs: 29164 / % possible obs: 8.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.18-3.5197.9
3.5-41100
4-51100
5-61100
6-10184.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U9N

1u9n


Resolution: 3.2→19 Å / Cor.coef. Fo:Fc: 0.784 / Cor.coef. Fo:Fc free: 0.612 / SU B: 73.889 / SU ML: 0.53 / Cross valid method: THROUGHOUT / ESU R Free: 0.629 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31768 216 5 %RANDOM
Rwork0.23961 ---
obs0.24378 4119 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: 18.011 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 0 0 1520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221554
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9432121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.25223.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.55815243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0521513
X-RAY DIFFRACTIONr_chiral_restr0.090.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211200
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3051.5970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59821559
X-RAY DIFFRACTIONr_scbond_it0.8593584
X-RAY DIFFRACTIONr_scangle_it1.5464.5562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 3.2 Å / Num. reflection Rwork: 272 / Total num. of bins used: 20
Refinement TLS params.Method: refined / Origin x: 26.6867 Å / Origin y: 75.8561 Å / Origin z: 8.879 Å
111213212223313233
T0.0775 Å2-0.0492 Å20.0103 Å2-0.0722 Å20.0073 Å2--0.0256 Å2
L3.8485 °2-1.4674 °20.2168 °2-1.0766 °20.111 °2--1.0128 °2
S0.0055 Å °0.0229 Å °-0.061 Å °0.0062 Å °-0.0175 Å °0.0967 Å °-0.0694 Å °-0.1261 Å °0.012 Å °

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