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- PDB-6ho0: TRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN... -

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Basic information

Entry
Database: PDB / ID: 6ho0
TitleTRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH BDM41325
ComponentsHTH-type transcriptional regulator EthR
KeywordsDNA BINDING PROTEIN / HELIX-TURN-HELIX / TETR-FAMILY / COMPLEX / INHIBITOR / DRUG DESIGN / TUBERCULOSIS / ETHIONAMIDE
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
Chem-GFK / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWintjens, R. / Wohlkonig, A.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2018
Title: A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR.
Authors: Tanina, A. / Wohlkonig, A. / Soror, S.H. / Flipo, M. / Villemagne, B. / Prevet, H. / Deprez, B. / Moune, M. / Peree, H. / Meyer, F. / Baulard, A.R. / Willand, N. / Wintjens, R.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3682
Polymers24,9281
Non-polymers4401
Water75742
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7374
Polymers49,8562
Non-polymers8812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2870 Å2
ΔGint-20 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.385, 121.385, 33.715
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: 24927.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WMC1
#2: Chemical ChemComp-GFK / 4,4,4-tris(fluoranyl)-1-[4-[3-(6-methoxy-1,3-benzothiazol-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl]butan-1-one


Mass: 440.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19F3N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7 / Details: 1.4-1.6 ammonium sulfate, 15% glycerol, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→85.83 Å / Num. obs: 20525 / % possible obs: 99.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2888 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9N

1u9n


Resolution: 1.9→85.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.788 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22172 1024 5 %RANDOM
Rwork0.18201 ---
obs0.18396 19456 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→85.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 30 42 1535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131525
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171407
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.6712079
X-RAY DIFFRACTIONr_angle_other_deg1.5491.5893237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0725185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11121.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5815238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5561513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
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_it2.7552.941746
X-RAY DIFFRACTIONr_mcbond_other2.7152.937745
X-RAY DIFFRACTIONr_mcangle_it3.6154.389929
X-RAY DIFFRACTIONr_mcangle_other3.6214.393930
X-RAY DIFFRACTIONr_scbond_it4.0233.405779
X-RAY DIFFRACTIONr_scbond_other4.0223.406777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.914.9271151
X-RAY DIFFRACTIONr_long_range_B_refined6.89435.0061766
X-RAY DIFFRACTIONr_long_range_B_other6.88934.9471759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 72 -
Rwork0.298 1357 -
obs--96.75 %

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