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

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Basic information

Entry
Database: PDB / ID: 5ioz
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with N-(cyclopentylmethyl)cyclopentanecarboxamide at 2.02A resolution
ComponentsTetR-family transcriptional regulatory repressor protein
KeywordsTRANSCRIPTION / EthR / represor / boosting effect
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription
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-(cyclopentylmethyl)cyclopentanecarboxamide / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 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 / 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: TetR-family transcriptional regulatory repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9772
Polymers23,7821
Non-polymers1951
Water43224
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)47,9544
Polymers47,5632
Non-polymers3912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2780 Å2
ΔGint-20 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.830, 121.830, 33.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-6C4 / N-(cyclopentylmethyl)cyclopentanecarboxamide


Mass: 195.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
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: 298 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: 2.02→40.61 Å / Num. obs: 17308 / % possible obs: 99.8 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Net I/σ(I): 18.2 / Num. measured all: 215947
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.02-2.0712.10.946199
9.03-40.618.70.04198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.53 Å
Translation2.5 Å38.53 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: 2.02→31.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.409 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 876 5.1 %RANDOM
Rwork0.1961 ---
obs0.1981 16392 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.62 Å2 / Biso mean: 30.641 Å2 / Biso min: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.02→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 14 24 1525
Biso mean--26.4 28.89 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9542110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3565194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94323.66271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42115234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9991512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211184
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 54 -
Rwork0.27 1038 -
all-1092 -
obs--98.91 %

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