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

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Basic information

Entry
Database: PDB / ID: 7ngd
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
Chem-UAB / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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)24,0562
Polymers23,7821
Non-polymers2741
Water2,018112
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1124
Polymers47,5632
Non-polymers5492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2750 Å2
ΔGint-24 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.445, 121.445, 33.717
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-525-

HOH

21A-600-

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-UAB / 4-methyl-~{N}-(4-phenylbutyl)piperidine-1-carboxamide


Mass: 274.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: Vapour diffusion

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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: 1.47→85.87 Å / Num. obs: 43625 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 10.4
Reflection shellResolution: 1.47→1.5 Å / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2131 / CC1/2: 0.767

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Processing

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

5nio


Resolution: 1.47→85.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1895 4.3 %RANDOM
Rwork0.1929 ---
obs0.1938 41673 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.98 Å2 / Biso mean: 27.12 Å2 / Biso min: 13.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0 Å2
2--0.86 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 1.47→85.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 20 112 1631
Biso mean--30.27 35.36 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131572
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171454
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.6432145
X-RAY DIFFRACTIONr_angle_other_deg2.3571.5683354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54721.46189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08415245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3861513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021793
X-RAY DIFFRACTIONr_gen_planes_other0.0410.02350
X-RAY DIFFRACTIONr_mcbond_it2.5822.719780
X-RAY DIFFRACTIONr_mcbond_other2.5722.716779
X-RAY DIFFRACTIONr_mcangle_it3.6464.071976
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.294 3156 -
obs--99.78 %

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