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

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Basic information

Entry
Database: PDB / ID: 5myr
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK735816A at 1.83A 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 / 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-UDY / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.828 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,5882
Polymers25,2591
Non-polymers3281
Water1,802100
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1754
Polymers50,5192
Non-polymers6572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2920 Å2
ΔGint-22 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.363, 121.363, 33.699
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

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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-UDY / 6-fluoranyl-~{N}-(4-pyridin-2-yl-1,3-thiazol-2-yl)-1,3-benzothiazol-2-amine


Mass: 328.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9FN4S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.828→121.363 Å / Num. all: 22975 / Num. obs: 22975 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 27.11 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.116 / Rsym value: 0.107 / Net I/av σ(I): 5.8 / Net I/σ(I): 17.4 / Num. measured all: 290306
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.83-1.93131.4390.50.4271.5481.43999.8
1.93-2.0412.80.840.90.2510.9030.84100
2.04-2.1912.80.5151.40.1540.5540.515100
2.19-2.36130.312.40.0920.3320.31100
2.36-2.5912.80.1943.90.0580.2090.194100
2.59-2.8912.70.1355.50.0410.1450.135100
2.89-3.3412.60.0838.70.0250.090.083100
3.34-4.0912.20.054120.0170.0590.054100
4.09-5.7811.80.04512.80.0140.0490.045100
5.78-121.36310.70.03614.60.0120.0390.03699.9

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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: 1.828→85.817 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.2025 1175 5.13 %
Rwork0.1754 --
obs0.1768 22915 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.74 Å2 / Biso mean: 39.2909 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 1.828→85.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 22 100 1615
Biso mean--72.54 45.85 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071549
X-RAY DIFFRACTIONf_angle_d0.8852115
X-RAY DIFFRACTIONf_chiral_restr0.044241
X-RAY DIFFRACTIONf_plane_restr0.005275
X-RAY DIFFRACTIONf_dihedral_angle_d14.153910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8284-1.91160.27981360.252426552791
1.9116-2.01240.28551540.223726662820
2.0124-2.13850.23271450.184726672812
2.1385-2.30370.22821280.180926752803
2.3037-2.53550.2091690.162426872856
2.5355-2.90240.19631370.174127132850
2.9024-3.65680.17811490.168727652914
3.6568-85.91120.18831570.166429123069
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)
12.5014-2.01982.03879.415-2.33557.6955-0.12350.25320.2167-0.7939-0.0516-0.8888-0.19360.69680.23480.4423-0.14240.06170.3070.00020.3432-20.8602-52.735-4.9522
26.97454.5081-2.19223.9877-4.02828.13710.21460.514-0.1547-1.22860.46891.54460.0588-0.6119-0.35820.5346-0.1231-0.26880.41540.10430.6998-32.0276-46.4416-8.6736
31.85831.0196-0.12396.53510.29095.2013-0.25270.11110.3071-0.38680.32010.6582-0.5102-0.1633-0.09840.5944-0.24660.08770.2440.01660.3721-28.5311-58.5865-1.1288
49.94435.26481.16225.9671.56744.21830.1479-0.1257-0.26430.5302-0.0593-0.08450.89570.1349-0.1920.42940.07270.01340.14510.02270.2102-14.6159-41.50413.3391
50.9718-0.42821.37985.59450.45882.16690.572-0.47021.03-0.2232-0.3929-1.41260.221.35170.14740.47390.06370.32610.97310.08081.0744.2527-26.67660.4068
66.1532.12381.41147.00874.33077.19320.0542-0.00220.0988-0.14880.2506-0.7432-0.05290.4333-0.30910.23650.09020.02990.22330.00010.2526-7.496-27.8131-2.7772
78.6466-1.2627-6.98213.06971.39829.07740.276-0.26590.6007-0.17320.02810.7075-0.0475-0.4001-0.28430.4435-0.06080.02370.269-0.02540.4625-25.106-38.0231-2.093
82.79612.61370.93056.84381.61313.16840.088-0.2654-0.14520.5343-0.0741-0.1810.350.1969-0.01120.23420.08850.00680.24470.01380.16-12.3008-25.550310.2063
92.29171.07322.93732.44042.21878.1930.031-0.04540.02050.0188-0.00130.06680.1931-0.15020.02130.17670.03980.00720.18420.00870.1963-18.5667-24.51961.5147
102.8993-0.057-3.66562.38982.16146.47460.21680.7687-0.3304-0.1811-0.47920.78930.2291-0.81680.27870.26550.0449-0.07910.3567-0.09220.3255-24.548-25.3526-12.0797
115.61582.73584.15993.08521.40523.2928-0.07590.25030.018-0.14960.1106-0.0739-0.06560.3524-0.05730.15920.04090.03530.19880.01960.1793-10.8122-18.5289-3.7033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 38 )A22 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 46 )A39 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 67 )A47 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 92 )A68 - 92
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 98 )A93 - 98
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 115 )A99 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 131 )A116 - 131
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 167 )A132 - 167
9X-RAY DIFFRACTION9chain 'A' and (resid 168 through 187 )A168 - 187
10X-RAY DIFFRACTION10chain 'A' and (resid 188 through 195 )A188 - 195
11X-RAY DIFFRACTION11chain 'A' and (resid 196 through 214 )A196 - 214

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