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- PDB-6ho7: TRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN... -

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Basic information

Entry
Database: PDB / ID: 6ho7
TitleTRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH BDM44814
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
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
~{N}-[3,3,3-tris(fluoranyl)propyl]benzamide / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)25,1452
Polymers24,9281
Non-polymers2171
Water21612
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2904
Polymers49,8562
Non-polymers4342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2750 Å2
ΔGint-22 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.967, 120.967, 33.697
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 CDC1551 (bacteria)
Gene: ethR, etaR, MT3970 / Variant: CDC 1551 / Oshkosh / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WMC0
#2: Chemical ChemComp-GHQ / ~{N}-[3,3,3-tris(fluoranyl)propyl]benzamide


Mass: 217.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10F3NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
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: 2.5→33.7 Å / Num. obs: 9145 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1280 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
iMOSFLMdata reduction
MOLREPphasing
RefinementResolution: 2.5→33.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.027 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 456 5 %RANDOM
Rwork0.18022 ---
obs0.1831 8657 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.707 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 15 12 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131536
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171418
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6552094
X-RAY DIFFRACTIONr_angle_other_deg1.3821.5783263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76621.39586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
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_it3.0833.999763
X-RAY DIFFRACTIONr_mcbond_other3.083.998762
X-RAY DIFFRACTIONr_mcangle_it4.4595.995952
X-RAY DIFFRACTIONr_mcangle_other4.4595.996953
X-RAY DIFFRACTIONr_scbond_it4.0884.488773
X-RAY DIFFRACTIONr_scbond_other4.0864.487774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2036.5211143
X-RAY DIFFRACTIONr_long_range_B_refined7.40646.671708
X-RAY DIFFRACTIONr_long_range_B_other7.40446.6571709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 33 -
Rwork0.219 613 -
obs--97 %

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