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

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Basic information

Entry
Database: PDB / ID: 5mxv
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK1107112A at 1.63A 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-K3T / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.626 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 24, 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)25,5742
Polymers25,2591
Non-polymers3151
Water1,946108
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1484
Polymers50,5192
Non-polymers6302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.230, 121.230, 33.842
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-436-

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 H37Rv (bacteria)
Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WMC1
#2: Chemical ChemComp-K3T / 3-chloranyl-~{N}-(4,5-dihydro-1,3-thiazol-2-yl)-6-fluoranyl-1-benzothiophene-2-carboxamide


Mass: 314.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8ClFN2OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 50.03 %
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: 1.626→121.23 Å / Num. all: 32415 / Num. obs: 32415 / % possible obs: 100 % / Redundancy: 22 % / Biso Wilson estimate: 25.1 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.099 / Rsym value: 0.096 / Net I/av σ(I): 5.3 / Net I/σ(I): 26.6 / Num. measured all: 713630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.626-1.7111.71.0350.80.3261.1261.03599.9
1.71-1.8215.20.9540.70.2391.0060.954100
1.82-1.9426.20.9060.70.180.9320.906100
1.94-2.1260.4261.60.0850.4390.426100
2.1-2.325.80.2342.90.0470.2410.234100
2.3-2.5725.80.144.90.0280.1450.14100
2.57-2.9725.60.0986.80.020.1010.098100
2.97-3.6324.90.0699.30.0140.0710.069100
3.63-5.1423.30.05411.70.0110.0560.054100
5.14-121.2321.40.04413.20.010.0450.04499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å85.72 Å
Translation2.5 Å85.72 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.626→85.723 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 17.15
RfactorNum. reflection% reflection
Rfree0.1919 1643 5.08 %
Rwork0.1701 --
obs0.1712 32356 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.52 Å2 / Biso mean: 39.4254 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 1.626→85.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 19 108 1611
Biso mean--40.04 46.22 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061536
X-RAY DIFFRACTIONf_angle_d0.7832098
X-RAY DIFFRACTIONf_chiral_restr0.042241
X-RAY DIFFRACTIONf_plane_restr0.006271
X-RAY DIFFRACTIONf_dihedral_angle_d18.092905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6265-1.67430.28841390.245725072646
1.6743-1.72840.26841110.220625132624
1.7284-1.79020.21431220.208525352657
1.7902-1.86190.20831390.193225182657
1.8619-1.94660.18331460.174324922638
1.9466-2.04920.18021440.163325232667
2.0492-2.17760.18351520.160325202672
2.1776-2.34580.18891370.157725512688
2.3458-2.58190.18121310.15825872718
2.5819-2.95550.18871580.173325522710
2.9555-3.72360.19091260.163926422768
3.7236-85.84180.1891380.168527732911
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)
12.0096-3.09261.92978.0474-4.55393.3943-0.19640.4935-0.058-0.8609-0.0841-0.42560.57520.8810.29340.6292-0.13360.07940.3408-0.01390.4146-20.7818-52.4494-5.1551
25.45542.5941-2.14544.9425-4.46068.58560.52250.5358-0.3142-0.97610.28031.38421.1127-1.3366-0.5010.545-0.1439-0.23710.45650.17530.7466-31.9121-46.4279-8.7008
33.01450.365-0.46646.2477-1.21913.6149-0.32080.09220.2683-0.44230.55890.6203-0.3096-0.2343-0.31140.8281-0.41220.13270.20570.07640.4196-28.3662-58.54-1.1562
45.84795.71691.24295.53591.52261.68170.2116-0.1628-0.44120.5217-0.0898-0.22890.84050.1499-0.20480.51940.04720.01550.23950.03070.3425-14.5892-41.42463.3215
50.86650.43950.2791.15660.90420.7120.66140.1630.5032-0.6458-0.102-0.9779-0.18230.6727-0.33990.63390.16010.32840.9345-0.00960.99683.9952-26.7830.534
66.76991.94741.22957.08253.97888.2565-0.08260.03520.144-0.12150.324-0.66990.0520.6829-0.21670.20980.08720.01830.2163-0.01310.2355-7.4647-27.7183-2.7559
74.8402-1.046-5.09522.59720.98985.3540.09260.07510.1015-0.19340.07250.65730.1787-0.5447-0.15370.3994-0.08890.00320.28280.0060.473-24.9184-37.9856-2.0066
86.34874.62351.12878.52741.35073.92620.0486-0.4053-0.22240.4767-0.0717-0.1110.50290.16820.02470.26890.10330.02950.22520.0140.1658-14.2395-29.229410.0283
98.0532-0.01341.90833.1536-2.26623.3586-0.2806-0.0864-0.30570.09530.4222-0.4794-0.45060.6652-0.10480.2645-0.0241-0.02130.4036-0.1450.3394-5.6724-12.887510.8713
102.720.3592.72793.05342.62917.99880.0377-0.0464-0.0650.03080.02620.05210.23830.0146-0.05610.16980.02170.02080.17110.01040.1929-18.7003-24.69791.1633
114.31440.1607-3.13733.53782.10343.6756-0.04480.78090.3671-0.437-0.49120.89120.0584-1.20990.54660.29060.0186-0.03430.4167-0.07810.331-24.43-24.6776-12.1131
124.39661.20322.97072.34771.90139.38820.00210.1490.1169-0.10820.121-0.1395-0.05060.4484-0.14280.14960.03120.02880.20230.00780.2244-10.7152-18.7779-3.9231
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 158 )A132 - 158
9X-RAY DIFFRACTION9chain 'A' and (resid 159 through 167 )A159 - 167
10X-RAY DIFFRACTION10chain 'A' and (resid 168 through 188 )A168 - 188
11X-RAY DIFFRACTION11chain 'A' and (resid 189 through 195 )A189 - 195
12X-RAY DIFFRACTION12chain 'A' and (resid 196 through 214 )A196 - 214

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