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

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Basic information

Entry
Database: PDB / ID: 5myn
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK445886A at 1.56A 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-ZUF / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.564 Å
AuthorsBlaszczyk, M. / Mendes, V. / Mugumbate, G. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United Kingdom
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)25,5482
Polymers25,2591
Non-polymers2891
Water2,162120
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0964
Polymers50,5192
Non-polymers5782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.813, 121.813, 33.700
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-423-

HOH

21A-508-

HOH

31A-519-

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-ZUF / ~{N}-(5-chloranylpyridin-2-yl)-4-pyridin-2-yl-1,3-thiazol-2-amine


Mass: 288.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClN4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
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: 1.564→43.067 Å / Num. all: 36051 / Num. obs: 36051 / % possible obs: 98.8 % / Redundancy: 11 % / Biso Wilson estimate: 23.28 Å2 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Rsym value: 0.054 / Net I/av σ(I): 7.8 / Net I/σ(I): 26 / Num. measured all: 396526
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.564-1.655.50.76710.3870.9350.76792.4
1.65-1.7580.551.40.2180.6260.5599.7
1.75-1.8712.70.3821.80.1150.410.382100
1.87-2.0212.80.2212.80.0660.2360.221100
2.02-2.2113.10.1185.50.0350.1250.118100
2.21-2.4712.70.0758.80.0230.080.075100
2.47-2.8612.80.05411.80.0160.0580.054100
2.86-3.5120.04114.70.0130.0450.041100
3.5-4.9511.60.036160.0110.0390.036100
4.95-43.06710.80.03117.20.010.0340.03199.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.564→43.067 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1947 1801 5 %
Rwork0.1697 --
obs0.171 35991 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.73 Å2 / Biso mean: 36.3604 Å2 / Biso min: 14.16 Å2
Refinement stepCycle: final / Resolution: 1.564→43.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 19 120 1631
Biso mean--37.35 44.45 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061544
X-RAY DIFFRACTIONf_angle_d0.7132106
X-RAY DIFFRACTIONf_chiral_restr0.045241
X-RAY DIFFRACTIONf_plane_restr0.004274
X-RAY DIFFRACTIONf_dihedral_angle_d12.588910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5639-1.60620.29281050.27692249235485
1.6062-1.65350.23881190.23162517263697
1.6535-1.70680.20331250.2072627275299
1.7068-1.76780.21291330.189226352768100
1.7678-1.83860.18581420.169726122754100
1.8386-1.92230.18351290.171526412770100
1.9223-2.02360.18951640.166826202784100
2.0236-2.15040.19061590.156526342793100
2.1504-2.31640.17921450.159926532798100
2.3164-2.54950.18161500.158226692819100
2.5495-2.91840.19751460.166427002846100
2.9184-3.67660.18111380.16927392877100
3.6766-43.08370.2061460.167128943040100
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)
12.03210.31480.42766.0687-0.64313.8602-0.02810.5312-0.366-0.2715-0.08080.13820.6705-0.26150.0050.22610.0675-0.00480.4778-0.05210.3226-53.224621.1751-13.5275
25.7821-0.0051-1.37060.92030.59770.95990.14220.54511.018-0.1648-0.1586-0.1652-0.5582-0.3034-0.08780.28770.19530.04520.5373-0.00420.4725-55.793229.4369-11.8022
38.0268-5.15571.00923.3145-0.33432.702-0.0533-0.3851-0.22180.2130.07150.35320.2336-0.7727-0.02380.1767-0.06970.02080.4093-0.02670.2494-41.847514.7871-5.1302
40.0043-0.00460.0050.0019-0.01030.0064-0.56220.2313-0.86940.11720.2506-0.02380.7459-0.41270.31590.7647-0.01220.07330.5551-0.24271.1698-27.0162-4.0492-7.887
53.4408-0.78280.38094.25050.59812.69980.14870.120.0377-0.0235-0.12050.0620.0734-0.2981-0.04280.1806-0.04750.03050.247-0.01550.213-32.203614.3617-11.3503
64.8244-1.26950.82312.1412-0.18213.02410.0967-0.32-0.10130.1805-0.07870.09490.2289-0.2671-0.04610.2291-0.07860.01280.2046-0.00930.1559-26.579713.5471.5409
72.19640.20340.43911.5715-0.36483.09420.00620.10130.0443-0.08170.02140.0693-0.0014-0.0545-0.01030.1732-0.0334-0.00340.1478-0.00630.163-22.524916.5624-11.1111
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 67 )A39 - 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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