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- PDB-7ngt: Mycobacterium tuberculosis transcriptional regulator EthR with bo... -

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Basic information

Entry
Database: PDB / ID: 7ngt
TitleMycobacterium tuberculosis transcriptional regulator EthR with bound inhibitory compound
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / ETHR / Tuberculosis / Inhibition
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 / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
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 / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsTomlinson, C.W.E. / Tatum, N.J. / Pohl, E.
CitationJournal: To Be Published
Title: Systematic exploration of the hydrophobic capacity of the EthR binding site for lead compound optimization
Authors: Tatum, N.J. / Tomlinson, C.W.E. / Frita, R. / Bennett, R. / Baulard, A.R. / Pohl, E. / Kitching, M.O.
History
DepositionFeb 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
Water905
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 area3170 Å2
ΔGint-46 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.776, 120.776, 33.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-403-

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 BL21(DE3) (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: PEG based

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→42.74 Å / Num. obs: 9245 / % possible obs: 99.8 % / Redundancy: 11.3 % / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 2.49→2.59 Å / Mean I/σ(I) obs: 5.7 / Num. unique obs: 1015 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NIO

5nio


Resolution: 2.49→42.74 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.425 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 490 5.3 %RANDOM
Rwork0.22 ---
obs0.2219 8722 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 31.484 Å2 / Biso min: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å2-0 Å2-0 Å2
2--1.72 Å2-0 Å2
3----3.45 Å2
Refinement stepCycle: final / Resolution: 2.49→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 19 5 1523
Biso mean--48.27 22.59 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131548
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171436
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6432109
X-RAY DIFFRACTIONr_angle_other_deg2.3241.5683306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28921.26487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31615240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5451513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0450.02341
X-RAY DIFFRACTIONr_mcbond_it2.4963.306771
X-RAY DIFFRACTIONr_mcbond_other2.4873.304770
X-RAY DIFFRACTIONr_mcangle_it3.9374.956962
LS refinement shellResolution: 2.49→2.554 Å
RfactorNum. reflection% reflection
Rfree0.272 39 -
Rwork0.234 615 -
obs--96.75 %

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