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- PDB-5nio: EthR complex -

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Basic information

Entry
Database: PDB / ID: 5nio
TitleEthR complex
ComponentsHTH-type transcriptional regulator EthR
KeywordsDNA BINDING PROTEIN / TetR repressor / protein ligand complex
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
~{N}-butyl-4-methyl-piperidine-1-carboxamide / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsPohl, E. / Tatum, N.J. / Cole, J.C. / Baulard, A.R.
CitationJournal: 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 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 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)24,0763
Polymers23,7821
Non-polymers2942
Water2,162120
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1526
Polymers47,5632
Non-polymers5894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3160 Å2
ΔGint-48 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.083, 120.083, 33.659
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-416-

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-8YH / ~{N}-butyl-4-methyl-piperidine-1-carboxamide


Mass: 198.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22N2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES buffer, 1.4-1.6 M AS / PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.4→84.91 Å / Num. obs: 48919 / % possible obs: 99.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 22.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.4 / Num. unique obs: 16586 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.4→84.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.935 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20498 2397 4.9 %RANDOM
Rwork0.18096 ---
obs0.18214 46522 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.4→84.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 19 120 1635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021640
X-RAY DIFFRACTIONr_bond_other_d0.0020.021557
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9492257
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0033575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.52123.97478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35815260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3741513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02392
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_it2.7842.367805
X-RAY DIFFRACTIONr_mcbond_other2.7782.365804
X-RAY DIFFRACTIONr_mcangle_it3.7993.541013
X-RAY DIFFRACTIONr_mcangle_other3.7983.5421014
X-RAY DIFFRACTIONr_scbond_it4.232.706835
X-RAY DIFFRACTIONr_scbond_other4.232.696832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0123.8981227
X-RAY DIFFRACTIONr_long_range_B_refined7.0419.4772004
X-RAY DIFFRACTIONr_long_range_B_other6.99219.1081953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 157 -
Rwork0.275 3294 -
obs--98.15 %

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