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- PDB-5ezh: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -

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Basic information

Entry
Database: PDB / ID: 5ezh
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 21 at 1.7A resolution
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / repressor / Mycobacterium tuberculosis
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
Chem-841 / HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSurade, S. / Blaszczyk, M. / Nikiforov, P.O. / Abell, C. / Blundell, T.L.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Bill & Melinda Gates Foundation United States
European Union
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters.
Authors: Nikiforov, P.O. / Surade, S. / Blaszczyk, M. / Delorme, V. / Brodin, P. / Baulard, A.R. / Blundell, T.L. / Abell, C.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)25,9324
Polymers25,2591
Non-polymers6733
Water88349
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8648
Polymers50,5192
Non-polymers1,3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3110 Å2
ΔGint-43 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.410, 121.410, 33.890
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-413-

HOH

21A-446-

HOH

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Components

#1: Protein HTH-type transcriptional regulator EthR


Mass: 25259.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, etaR, MT3970 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC0, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-841 / ~{N}-[(1-pyridin-2-ylpiperidin-4-yl)methyl]pyrrolidine-1-carboxamide


Mass: 288.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N4O
#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.: 49 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulphate, Glycerol, MES / PH range: 6.3 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.7→85.85 Å / Num. obs: 28584 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Net I/σ(I): 28.4 / Num. measured all: 359919
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.7412.60.8153.92600120560.8840.23699.9
7.6-85.859.60.02367.2382339810.00799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å85.85 Å
Translation2.5 Å85.85 Å

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.7→60.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2302 / WRfactor Rwork: 0.1884 / FOM work R set: 0.8655 / SU B: 1.671 / SU ML: 0.057 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.0974 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1443 5.1 %RANDOM
Rwork0.194 ---
obs0.1959 27091 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.27 Å2 / Biso mean: 28.56 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.7→60.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 47 49 1592
Biso mean--26.51 34.83 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021577
X-RAY DIFFRACTIONr_angle_refined_deg2.3471.9792148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8125192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31723.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6851513
X-RAY DIFFRACTIONr_chiral_restr0.1760.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211208
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 89 -
Rwork0.295 1775 -
all-1864 -
obs--99.95 %

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