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

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Basic information

Entry
Database: PDB / ID: 5ioy
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with N-(cyclopentylmethyl)pyrrolidine-1-carboxamide at 1.77A resolution
ComponentsTetR-family transcriptional regulatory repressor protein
KeywordsTRANSCRIPTION / EthR / represor / boosting effect
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
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 / Homeobox-like domain superfamily ...: / 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-(cyclopentylmethyl)pyrrolidine-1-carboxamide / TetR-family transcriptional regulatory repressor protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 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 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: TetR-family transcriptional regulatory repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4675
Polymers23,7821
Non-polymers6854
Water82946
1
A: TetR-family transcriptional regulatory repressor protein
hetero molecules

A: TetR-family transcriptional regulatory repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,93310
Polymers47,5632
Non-polymers1,3708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3060 Å2
ΔGint-43 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.350, 121.350, 33.850
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-402-

HOH

21A-445-

HOH

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Components

#1: Protein TetR-family transcriptional regulatory repressor protein


Mass: 23781.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Gene: ethR, MRA_3895 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U9I4
#2: Chemical ChemComp-6C5 / N-(cyclopentylmethyl)pyrrolidine-1-carboxamide


Mass: 196.289 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H20N2O
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
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: I04 / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS3 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: 1.77→42.9 Å / Num. obs: 25363 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Net I/σ(I): 24.7 / Num. measured all: 321676
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-1.8212.70.8452322518330.8840.2470.8813.999.9
7.92-42.99.70.025347135710.0080.02660.999

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.9 Å
Translation2.5 Å42.9 Å

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.77→42.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.815 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0991 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1293 5.1 %RANDOM
Rwork0.1841 ---
obs0.1857 24017 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.66 Å2 / Biso mean: 24.321 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.77→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 47 46 1580
Biso mean--28.55 28.44 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021567
X-RAY DIFFRACTIONr_angle_refined_deg2.4671.9772135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9815192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73823.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38115233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1391512
X-RAY DIFFRACTIONr_chiral_restr0.1820.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211189
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 97 -
Rwork0.25 1549 -
all-1646 -
obs--99.94 %

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