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

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Basic information

Entry
Database: PDB / ID: 5myt
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK921295A at 1.61A resolution
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / Mycobacterium tuberculosis / repressor
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-ZQC / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5872
Polymers25,2591
Non-polymers3271
Water2,018112
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1734
Polymers50,5192
Non-polymers6552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3000 Å2
ΔGint-21 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.167, 121.167, 33.716
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-420-

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


Mass: 327.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N3OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 49.79 %
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: 1.61→38.316 Å / Num. all: 32287 / Num. obs: 32287 / % possible obs: 97.5 % / Redundancy: 11.6 % / Biso Wilson estimate: 24 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.096 / Rsym value: 0.089 / Net I/av σ(I): 5.3 / Net I/σ(I): 20.3 / Num. measured all: 375730
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.61-1.77.71.4940.50.5771.6911.49484.1
1.7-1.810.41.1760.60.3831.2771.17699.2
1.8-1.9213.20.8110.80.2330.8580.811100
1.92-2.0812.50.4011.60.1190.4250.401100
2.08-2.2813.20.2312.90.0670.2450.231100
2.28-2.5512.30.144.80.0430.150.14100
2.55-2.9412.80.0917.30.0270.0980.091100
2.94-3.611.80.0610.20.0190.0650.06100
3.6-5.0911.30.04812.30.0150.0530.048100
5.09-38.31610.80.041120.0130.0440.04199.6

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Processing

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

1t56


Resolution: 1.61→38.316 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.91
RfactorNum. reflection% reflection
Rfree0.1785 1623 5.04 %
Rwork0.1683 --
obs0.1688 32185 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.31 Å2 / Biso mean: 38.3314 Å2 / Biso min: 14.91 Å2
Refinement stepCycle: final / Resolution: 1.61→38.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 22 112 1624
Biso mean--44.26 46.41 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051545
X-RAY DIFFRACTIONf_angle_d0.7522108
X-RAY DIFFRACTIONf_chiral_restr0.047241
X-RAY DIFFRACTIONf_plane_restr0.005275
X-RAY DIFFRACTIONf_dihedral_angle_d12.936908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6103-1.65770.3171910.27371966205777
1.6577-1.71120.2891300.24762283241389
1.7112-1.77240.21821400.2112571271199
1.7724-1.84330.19121310.185925592690100
1.8433-1.92720.18921250.169725912716100
1.9272-2.02880.16471380.155325952733100
2.0288-2.15590.16711390.150125992738100
2.1559-2.32230.16191480.154826052753100
2.3223-2.5560.1831390.159526402779100
2.556-2.92580.19031590.1726242783100
2.9258-3.68570.16341320.168426982830100
3.6857-38.32720.17071510.163728312982100
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)
15.2731-1.13021.22384.7885-0.26584.54520.2278-1.1434-0.46950.3141-0.07390.1156-0.1014-0.34150.00350.2916-0.1521-0.01120.51750.0340.3657-50.2601-24.62736.303
23.5090.3988-0.25450.92080.95083.71520.2221-0.3768-0.45750.149-0.0338-0.15290.06520.5075-0.07860.2786-0.1946-0.01850.5405-0.06420.3688-58.2922-28.61141.1202
34.96474.7517-0.89988.4592-0.30632.0268-0.05720.48280.0882-0.09390.15860.1688-0.1149-0.7669-0.02840.19110.0357-0.02970.4225-0.01270.2504-41.3692-14.6306-3.3856
40.4413-0.44470.21020.4457-0.21340.098-0.2935-0.18570.3928-0.02020.13670.0877-0.3344-0.17020.36171.00180.04470.02880.4873-0.29890.9663-26.59894.3215-0.5471
53.25681.0023-0.15793.71880.06432.76120.0477-0.1386-0.0853-0.0802-0.0309-0.0728-0.0418-0.3522-0.09020.16080.0397-0.01160.2541-0.00770.2039-31.5345-14.03942.8974
63.36630.65980.02412.10920.34352.72850.05180.22710.0356-0.2309-0.08750.0655-0.1665-0.26350.0310.23060.0749-0.00570.2291-0.00660.1628-26.0443-13.2222-9.9851
71.4825-0.2381-0.01341.3878-0.10471.98660.0074-0.0736-0.00140.07380.02860.0194-0.0268-0.1121-0.01950.1810.03850.00090.1709-0.00750.1672-22.0474-16.10942.701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 46 )A22 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 67 )A47 - 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 129 )A99 - 129
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 167 )A130 - 167
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 214 )A168 - 214

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