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- PDB-5j1u: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -

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Basic information

Entry
Database: PDB / ID: 5j1u
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with N-(furan-3-ylmethyl)pyrrolidine-1-carboxamide at 1.80A resolution
ComponentsEthR
KeywordsTRANSCRIPTION / EthR / represor / boosting effect
Function / homology
Function and homology information


monooxygenase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / 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
N-[(furan-3-yl)methyl]pyrrolidine-1-carboxamide / Mutant monooxygenase EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBlaszczyk, M. / Surade, S. / 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: ACS Chem. Biol. / Year: 2017
Title: Fragment-Sized EthR Inhibitors Exhibit Exceptionally Strong Ethionamide Boosting Effect in Whole-Cell Mycobacterium tuberculosis Assays.
Authors: Nikiforov, P.O. / Blaszczyk, M. / Surade, S. / Boshoff, H.I. / Sajid, A. / Delorme, V. / Deboosere, N. / Brodin, P. / Baulard, A.R. / Barry, C.E. / Blundell, T.L. / Abell, C.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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: EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9762
Polymers23,7821
Non-polymers1941
Water63135
1
A: EthR
hetero molecules

A: EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9524
Polymers47,5632
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2740 Å2
ΔGint-23 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.376, 121.376, 33.718
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-410-

HOH

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Components

#1: Protein EthR / Mutant monooxygenase EthR / TetR family transcriptional regulator


Mass: 23781.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: ethR_2, ethR, ethR_1, AFL40_4013, BN1213_00375, BN1303_02839, ERS007657_00006, ERS007665_03402, ERS007670_00101, ERS007672_00126, ERS007679_01009, ERS007681_01169, ERS007688_00760, ERS007703_ ...Gene: ethR_2, ethR, ethR_1, AFL40_4013, BN1213_00375, BN1303_02839, ERS007657_00006, ERS007665_03402, ERS007670_00101, ERS007672_00126, ERS007679_01009, ERS007681_01169, ERS007688_00760, ERS007703_00420, ERS007722_01164, ERS007741_02569, ERS013447_02283, ERS013471_02551, ERS023446_02032, ERS024213_01441, ERS024276_01130, ERS027644_00684, ERS027646_02322, ERS027654_00374, ERS027656_00876, ERS031537_01716, ERS075357_02728, ERS075361_00362, ERS075387_01097, ERS124361_02860, IQ38_20160, IQ40_19545, IQ45_19480, IQ47_19420, IU13_19735, IU16_19625
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KCS8, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-P93 / N-[(furan-3-yl)methyl]pyrrolidine-1-carboxamide


Mass: 194.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / 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: I03 / Wavelength: 0.983 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.79→85.84 Å / Num. obs: 24439 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 22.5 / Num. measured all: 307350 / Scaling rejects: 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.79-1.8412.60.814199.9
8.01-85.849.80.025199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.8→26.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.158 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1228 5.1 %RANDOM
Rwork0.1977 ---
obs0.1995 22819 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.68 Å2 / Biso mean: 29.047 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.8→26.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 14 35 1536
Biso mean--25.98 30.28 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021533
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9552091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8365192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85923.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4341512
X-RAY DIFFRACTIONr_chiral_restr0.1480.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211179
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 78 -
Rwork0.292 1430 -
all-1508 -
obs--95.69 %

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