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

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Basic information

Entry
Database: PDB / ID: 6hoc
TitleTRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH BDM44847
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


regulation of DNA-templated transcription / DNA binding
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-GJE / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Jan 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)25,1862
Polymers24,9281
Non-polymers2581
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)50,3724
Polymers49,8562
Non-polymers5162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2750 Å2
ΔGint-21 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.532, 121.532, 33.822
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-402-

HOH

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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-GJE / 4-azido-~{N}-[3,3,3-tris(fluoranyl)propyl]benzamide


Mass: 258.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9F3N4O
#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: 2.41 Å3/Da / Density % sol: 48.98 %
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→33.82 Å / Num. obs: 9272 / % possible obs: 99.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.3
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 6 / Num. unique obs: 1270 / % possible all: 95.1

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Processing

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

1u9n


Resolution: 2.5→33.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.552 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22841 461 5 %RANDOM
Rwork0.18202 ---
obs0.18442 8780 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.5→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 18 12 1485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171393
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6562044
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5773202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9721.1984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36815237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0041513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
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_it2.7793.402742
X-RAY DIFFRACTIONr_mcbond_other2.743.4741
X-RAY DIFFRACTIONr_mcangle_it3.9335.096924
X-RAY DIFFRACTIONr_mcangle_other3.9325.098925
X-RAY DIFFRACTIONr_scbond_it3.9893.845760
X-RAY DIFFRACTIONr_scbond_other3.8013.838759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7655.5671121
X-RAY DIFFRACTIONr_long_range_B_refined7.0839.4381669
X-RAY DIFFRACTIONr_long_range_B_other7.0839.4331669
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 30 -
Rwork0.181 577 -
obs--90.6 %

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