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

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Basic information

Entry
Database: PDB / ID: 5myl
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK1570606A at 1.72A resolution
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / Mycobacterium tuberculosis / represor
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 / 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
Chem-Q2N / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.724 Å
AuthorsBlaszczyk, M. / Mendes, V. / Mugumbate, G. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Front Pharmacol / Year: 2017
Title: Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach.
Authors: Mugumbate, G. / Mendes, V. / Blaszczyk, M. / Sabbah, M. / Papadatos, G. / Lelievre, J. / Ballell, L. / Barros, D. / Abell, C. / Blundell, T.L. / Overington, J.P.
History
DepositionJan 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 17, 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 / citation / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _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)25,5732
Polymers25,2591
Non-polymers3131
Water1,29772
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1454
Polymers50,5192
Non-polymers6272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2820 Å2
ΔGint-22 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.659, 120.659, 33.660
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-421-

HOH

21A-470-

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 (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WMC1
#2: Chemical ChemComp-Q2N / 2-(4-fluorophenyl)-~{N}-(4-pyridin-2-yl-1,3-thiazol-2-yl)ethanamide


Mass: 313.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12FN3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.7 to 2.1 ammonium sulfate 0.1M MES (pH 6 to 7) 5 to 15%(v/v) glycerol 7 to 12%(v/v) 1,4-dioxane
PH range: pH range 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.724→42.659 Å / Num. all: 26955 / Num. obs: 26955 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 29.69 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.084 / Rsym value: 0.077 / Net I/av σ(I): 5.5 / Net I/σ(I): 18.7 / Num. measured all: 331256
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.724-1.8211.41.2770.60.4071.3921.277100
1.82-1.9313.10.77610.230.8340.776100
1.93-2.0612.50.4051.80.1220.4340.405100
2.06-2.2313.10.24730.0730.2640.247100
2.23-2.4412.40.1554.70.0480.1680.155100
2.44-2.7312.60.1076.90.0330.1160.107100
2.73-3.15120.0788.90.0250.0850.078100
3.15-3.8511.80.05910.40.0190.0650.059100
3.85-5.4511.30.05211.80.0160.0560.052100
5.45-42.65910.90.03913.10.0120.0410.03999.8

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.724→28.559 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.2151 1350 5.02 %
Rwork0.1826 --
obs0.1842 26884 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.59 Å2 / Biso mean: 44.3537 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 1.724→28.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 22 72 1592
Biso mean--71.96 46.4 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061553
X-RAY DIFFRACTIONf_angle_d0.7352118
X-RAY DIFFRACTIONf_chiral_restr0.044241
X-RAY DIFFRACTIONf_plane_restr0.004277
X-RAY DIFFRACTIONf_dihedral_angle_d14.991915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7238-1.78540.40741110.34325252636
1.7854-1.85690.26731370.252724872624
1.8569-1.94140.25861280.216825042632
1.9414-2.04370.22561360.196325152651
2.0437-2.17170.21661450.186725042649
2.1717-2.33930.19391260.182725412667
2.3393-2.57460.20471390.176925542693
2.5746-2.94680.20521490.17625422691
2.9468-3.71140.22081280.18326162744
3.7114-28.5630.2031510.166627462897
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.96810.85160.23112.0045-0.04280.4850.00220.214-0.0998-0.4973-0.07780.68340.0043-0.84630.21670.5977-0.1677-0.03460.3633-0.00570.396621.106352.1719-5.4026
20.38890.32580.65243.56840.92941.1457-0.24690.2933-0.16510.07250.0347-0.9636-0.28010.71960.0670.5905-0.2156-0.05690.403-0.03640.503729.531554.9337-2.8069
38.51914.9403-0.83555.2536-0.92542.30260.3328-0.24270.16330.6918-0.12970.0665-0.9422-0.0386-0.17240.54990.0547-0.0060.2501-0.03860.333314.383741.07893.3454
40.7596-0.8924-0.47181.11980.58280.32970.3377-0.1519-0.0807-0.0125-0.23640.31950.0436-0.4368-0.12730.52270.1285-0.20211.0769-0.29861.225-4.666826.21230.6258
53.65890.60270.29453.1081-0.36422.20670.09430.0249-0.22290.1234-0.0414-0.085-0.33040.0433-0.00340.30860.0475-0.04070.185600.261813.368331.2385-3.0365
62.1391.24220.27923.7371-0.39442.77490.0454-0.3065-0.00910.4309-0.0717-0.0341-0.2949-0.109-0.04210.29370.1042-0.01330.2507-0.01990.199713.151825.87169.9073
71.1581-0.21040.01032.0403-0.23341.9950.03640.12320.0178-0.1059-0.0256-0.0282-0.1262-0.0084-0.04020.23710.083-0.00760.25920.0010.234315.745921.6991-2.6766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 39 )A22 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 67 )A40 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 92 )A68 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 98 )A93 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 128 )A99 - 128
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 167 )A129 - 167
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 214 )A168 - 214

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