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

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Basic information

Entry
Database: PDB / ID: 5eyr
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 5 at 1.57A resolution
ComponentsEthRRoth Air Base
KeywordsTRANSCRIPTION / EthR / repressor / Mycobacterium tuberculosis
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 / 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
Chem-5T0 / Mutant monooxygenase EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 25, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)25,5892
Polymers25,2591
Non-polymers3291
Water3,063170
1
A: EthR
hetero molecules

A: EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1774
Polymers50,5192
Non-polymers6592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2840 Å2
ΔGint-22 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.885, 120.885, 33.829
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 EthR / Roth Air Base / Mutant monooxygenase EthR / TetR family transcriptional regulator / Transcriptional Regulatory ...Mutant monooxygenase EthR / TetR family transcriptional regulator / Transcriptional Regulatory Repressor Protein


Mass: 25259.254 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, ABI38_03425, AC434_03675, ACQ94_17905, ACQ95_03225, ACQ96_05940, AFL40_4013, BN1213_00375, BN1303_02839, ERS024750_01557, ERS024751_00529, ERS024758_02192, ERS024764_ ...Gene: ethR_2, ethR, ethR_1, ABI38_03425, AC434_03675, ACQ94_17905, ACQ95_03225, ACQ96_05940, AFL40_4013, BN1213_00375, BN1303_02839, ERS024750_01557, ERS024751_00529, ERS024758_02192, ERS024764_01791, ERS094182_00752, ERS124362_00364, ERS124821_00273, ERS124823_00877, ERS124824_02674, ERS124825_01051, ERS124826_00657, ERS124827_01397, ERS124828_02317, ERS124829_02606, ERS124830_02614, ERS124831_02648, ERS124832_01045, IQ38_20160, IQ40_19545, IQ45_19480, IQ47_19420, IU13_19735, IU16_19625, TL06_14095
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045KCS8, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-5T0 / 3-[1-[4-(methylaminomethyl)phenyl]piperidin-4-yl]-1-pyrrolidin-1-yl-propan-1-one


Mass: 329.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 295 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: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.57→85.48 Å / Num. obs: 34875 / % possible obs: 97.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Net I/σ(I): 29.6 / Num. measured all: 463192
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.57-1.7213.81.0012.810901978990.860.27794.5
3.85-85.4812.10.018112.631650262410.00598.6

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
BUSTER-TNTBUSTER 2.10.2refinement
PDB_EXTRACT3.15data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.57→21.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9391 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1779 5.11 %RANDOM
Rwork0.1859 ---
obs0.1868 34811 97.56 %-
Displacement parametersBiso max: 89.45 Å2 / Biso mean: 32.48 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.7102 Å20 Å20 Å2
2---2.7102 Å20 Å2
3---5.4205 Å2
Refine analyzeLuzzati coordinate error obs: 0.212 Å
Refinement stepCycle: final / Resolution: 1.57→21.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 24 170 1681
Biso mean--34.92 47.13 -
Num. residues----193
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d524SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes228HARMONIC5
X-RAY DIFFRACTIONt_it1544HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion208SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1908SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1544HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2106HARMONIC20.86
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion14.77
LS refinement shellResolution: 1.57→1.62 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2277 112 4.04 %
Rwork0.2159 2658 -
all0.2164 2770 -
obs--90.9 %

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