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- PDB-5f27: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -

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Basic information

Entry
Database: PDB / ID: 5f27
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 2 at 1.68A 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 / 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
~{N}-methyl-1-(4-piperidin-1-ylphenyl)methanamine / HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 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
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_symm_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_symm_contact.auth_seq_id_1
Revision 3.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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)25,6683
Polymers25,2591
Non-polymers4092
Water3,045169
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3366
Polymers50,5192
Non-polymers8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2740 Å2
ΔGint-23 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.170, 120.170, 33.630
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-447-

HOH

21A-542-

HOH

31A-545-

HOH

41A-552-

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-5TT / ~{N}-methyl-1-(4-piperidin-1-ylphenyl)methanamine


Mass: 204.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.684→84.973 Å / Num. all: 27668 / Num. obs: 27668 / % possible obs: 97.3 % / Redundancy: 8.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.081 / Rsym value: 0.076 / Net I/av σ(I): 5.799 / Net I/σ(I): 18.3 / Num. measured all: 238221
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.68-1.788.30.2862.33259839380.1020.286797.2
1.78-1.888.50.1853.53233237940.0660.1851098.1
1.88-2.018.80.1334.93127835710.0470.13313.798.5
2.01-2.1790.0966.63038733670.0340.09618.698.8
2.17-2.3890.0817.42830031340.0280.08121.899.2
2.38-2.669.10.0718.92574528340.0250.07124.999
2.66-3.079.10.0718.62314425400.0250.07126.999.4
3.07-3.778.50.0728.51831921530.0260.07228.898.4
3.77-5.337.10.0610.51113915660.0250.0626.691.5
5.33-42.4876.50.05511.249797710.0230.05523.474.1

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.684→42.487 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1401 5.07 %
Rwork0.199 26234 -
obs0.2004 27635 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69 Å2 / Biso mean: 28.4824 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.684→42.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 30 169 1649
Biso mean--28.2 42.07 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061511
X-RAY DIFFRACTIONf_angle_d0.8422055
X-RAY DIFFRACTIONf_chiral_restr0.043235
X-RAY DIFFRACTIONf_plane_restr0.009264
X-RAY DIFFRACTIONf_dihedral_angle_d14.574898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.684-1.74420.26021530.21832557271098
1.7442-1.8140.27011460.21822560270697
1.814-1.89660.2461430.20822594273797
1.8966-1.99660.24331320.20672617274998
1.9966-2.12170.2211290.19022646277598
2.1217-2.28550.21481390.19242650278999
2.2855-2.51540.21151420.19262684282699
2.5154-2.87940.21661470.19942696284399
2.8794-3.62740.23391490.19492722287199
3.6274-42.50.22461210.2022508262985

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