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

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Basic information

Entry
Database: PDB / ID: 7ngu
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-UAZ / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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)24,2224
Polymers23,7821
Non-polymers4403
Water3,099172
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4448
Polymers47,5632
Non-polymers8816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3480 Å2
ΔGint-84 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.968, 121.968, 33.728
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-444-

HOH

21A-526-

HOH

31A-548-

HOH

41A-556-

HOH

51A-564-

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-UAZ / ~{N}-(4-methoxyphenyl)-4-methyl-piperidine-1-carboxamide


Mass: 248.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.26→61.06 Å / Num. obs: 67886 / % possible obs: 98 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 15.3
Reflection shellResolution: 1.26→1.28 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2552 / CC1/2: 0.577

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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: 1.26→61.06 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 3306 4.9 %RANDOM
Rwork0.1898 ---
obs0.1909 64493 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.99 Å2 / Biso mean: 23.188 Å2 / Biso min: 10.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å2-0 Å2
2--0.69 Å2-0 Å2
3----1.38 Å2
Refinement stepCycle: final / Resolution: 1.26→61.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 28 172 1693
Biso mean--34.67 38.04 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131567
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171435
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.6422141
X-RAY DIFFRACTIONr_angle_other_deg2.3661.5673305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.575196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87221.74486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75315239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4611512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021777
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02347
X-RAY DIFFRACTIONr_mcbond_it2.0752.219775
X-RAY DIFFRACTIONr_mcbond_other2.0612.216774
X-RAY DIFFRACTIONr_mcangle_it3.0413.325968
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 183 -
Rwork0.306 3758 -
all-3941 -
obs--77.96 %

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