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- PDB-6r1s: EthR ligand complex -

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Basic information

Entry
Database: PDB / ID: 6r1s
TitleEthR ligand complex
ComponentsHTH-type transcriptional regulator EthR
KeywordsDNA BINDING PROTEIN / Transcriptional regulator Tuberculosis TetR Inhibitor
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-JPK / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPohl, E. / Tatum, N.
Citation
Journal: J Phys Chem Lett / Year: 2019
Title: Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds.
Authors: Tatum, N.J. / Duarte, F. / Kamerlin, S.C.L. / Pohl, E.
#1: Journal: Org.Biomol.Chem. / Year: 2017
Title: New active leads for tuberculosis booster drugs by structure-based drug discovery.
Authors: Tatum, N.J. / Liebeschuetz, J.W. / Cole, J.C. / Frita, R. / Herledan, A. / Baulard, A.R. / Willand, N. / Pohl, E.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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)24,1622
Polymers23,7821
Non-polymers3801
Water1,08160
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3244
Polymers47,5632
Non-polymers7612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2860 Å2
ΔGint-21 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.894, 120.894, 33.676
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-407-

HOH

21A-447-

HOH

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Components

#1: Protein HTH-type transcriptional regulator EthR


Mass: 23781.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC1
#2: Chemical ChemComp-JPK / 2-(3-methylphenyl)-~{N}-[[2-(oxan-4-yl)-7-oxidanyl-pyrazolo[1,5-a]pyrimidin-5-yl]methyl]ethanamide


Mass: 380.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES, 1.4-1.6 M Ammoniumsulfate / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 43521 / % possible obs: 98.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.8→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.56 / Num. unique obs: 11505 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NIM

5nim


Resolution: 1.8→29.44 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.981 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23498 1147 4.9 %RANDOM
Rwork0.20015 ---
obs0.20185 22258 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 28 60 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131581
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171453
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6652163
X-RAY DIFFRACTIONr_angle_other_deg1.5651.5973346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2785198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.821.70588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
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_it3.1073.488777
X-RAY DIFFRACTIONr_mcbond_other3.1063.485776
X-RAY DIFFRACTIONr_mcangle_it4.4535.223971
X-RAY DIFFRACTIONr_mcangle_other4.4515.227972
X-RAY DIFFRACTIONr_scbond_it3.8013.966804
X-RAY DIFFRACTIONr_scbond_other3.7993.969805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6265.7831190
X-RAY DIFFRACTIONr_long_range_B_refined8.89542.6061877
X-RAY DIFFRACTIONr_long_range_B_other8.88442.6011876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 83 -
Rwork0.291 1467 -
obs--90.43 %

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