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

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Basic information

Entry
Database: PDB / ID: 7ngm
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-UAK / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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)24,0282
Polymers23,7821
Non-polymers2461
Water1,31573
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0564
Polymers47,5632
Non-polymers4932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.416, 121.416, 33.709
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-514-

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-UAK / 4-methyl-~{N}-[(1~{R})-1-phenylethyl]piperidine-1-carboxamide


Mass: 246.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 52.91 %
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: 1.76→85.89 Å / Num. obs: 25735 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 11.5
Reflection shellResolution: 1.76→1.79 Å / Mean I/σ(I) obs: 0.93 / Num. unique obs: 1274 / CC1/2: 0.744

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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: 1.76→85.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1280 5 %RANDOM
Rwork0.2102 ---
obs0.2119 24403 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.57 Å2 / Biso mean: 30.561 Å2 / Biso min: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å2-0 Å2-0 Å2
2--1.03 Å2-0 Å2
3----2.06 Å2
Refinement stepCycle: final / Resolution: 1.76→85.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 18 73 1587
Biso mean--38.08 37.94 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131546
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171435
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.6432107
X-RAY DIFFRACTIONr_angle_other_deg2.3441.5683300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9015192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26621.16386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241513
X-RAY DIFFRACTIONr_chiral_restr0.1090.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021753
X-RAY DIFFRACTIONr_gen_planes_other0.0340.02346
X-RAY DIFFRACTIONr_mcbond_it2.8133.067771
X-RAY DIFFRACTIONr_mcbond_other2.7593.064770
X-RAY DIFFRACTIONr_mcangle_it3.8124.586962
LS refinement shellResolution: 1.76→1.805 Å
RfactorNum. reflection% reflection
Rfree0.34 83 -
Rwork0.32 1773 -
obs--99.73 %

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