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- PDB-8rcx: Crystal structure of the Mycobacterium tuberculosis regulator Vir... -

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Basic information

Entry
Database: PDB / ID: 8rcx
TitleCrystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the drug candidate alpibectir
ComponentsHTH-type transcriptional regulator VirS
KeywordsTRANSCRIPTION / ARAC FAMILY / TUBERCULOSIS / DNA BINDING PROTEIN / IN SITU PROTEOLYSIS
Function / homology
Function and homology information


cellular response to acidic pH / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
HTH-type transcriptional regulator AraC-type, N-terminal / Arabinose-binding domain of AraC transcription regulator, N-term / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
: / HTH-type transcriptional regulator VirS
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsEdoo, Z. / Frita, R. / Grosse, C. / Bourotte, M. / Moune, M. / Antoine, R. / Trebosc, V. / Schellhorn, B. / Dreneau, A. / Hofmann, L. ...Edoo, Z. / Frita, R. / Grosse, C. / Bourotte, M. / Moune, M. / Antoine, R. / Trebosc, V. / Schellhorn, B. / Dreneau, A. / Hofmann, L. / Kemmer, C. / Lociuro, S. / Dale, G.E. / Jung, F. / Perez-Herran, E. / Mendoza, A. / Rebollo Lopez, M.J. / Ghidelli-Disse, S. / Drewes, G. / Mathys, V. / Soetaert, K. / Megalizzi, V. / Wintjens, R. / Barros Aguirre, D. / Remuinan, M.D. / Gitzinger, M. / Deprez, B. / Willand, N. / Pieren, M. / Baulard, A.R.
Funding support Belgium, France, 2items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)CR40003580 Belgium
Agence Nationale de la Recherche (ANR)ANR-20-PAMR-0005 France
CitationJournal: To Be Published
Title: Clinical candidate alpibectir rejuvenates ethionamide for treating tuberculosis
Authors: Edoo, Z. / Frita, R. / Grosse, C. / Bourotte, M. / Moune, M. / Antoine, R. / Trebosc, V. / Schellhorn, B. / Dreneau, A. / Hofmann, L. / Kemmer, C. / Lociuro, S. / Dale, G.E. / Jung, F. / ...Authors: Edoo, Z. / Frita, R. / Grosse, C. / Bourotte, M. / Moune, M. / Antoine, R. / Trebosc, V. / Schellhorn, B. / Dreneau, A. / Hofmann, L. / Kemmer, C. / Lociuro, S. / Dale, G.E. / Jung, F. / Perez-Herran, E. / Mendoza, A. / Rebollo Lopez, M.J. / Ghidelli-Disse, S. / Drewes, G. / Mathys, V. / Soetaert, K. / Megalizzi, V. / Wintjens, R. / Barros Aguirre, D. / Remuinan, M.D. / Gitzinger, M. / Deprez, B. / Willand, N. / Pieren, M. / Baulard, A.R.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator VirS
B: HTH-type transcriptional regulator VirS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8114
Polymers89,1472
Non-polymers6642
Water4,954275
1
A: HTH-type transcriptional regulator VirS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9062
Polymers44,5731
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HTH-type transcriptional regulator VirS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9062
Polymers44,5731
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.313, 115.313, 70.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HTH-type transcriptional regulator VirS


Mass: 44573.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Proteolytic fragment: residues 4-208
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: virS / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WMJ3
#2: Chemical ChemComp-YPQ / 4,4,4-tris(fluoranyl)-1-[3-(trifluoromethyl)-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl]butan-1-one


Mass: 332.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14F6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.3 M sodium acetate trihydrate, 0.1 M Tris, pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG 500 MME, pH7.5, protein:alpibectir ratio 1:1, in situ proteolysis with subtilisin, temperature 293K, vapor diffusion

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.494→19.244 Å / Num. obs: 78828 / % possible obs: 96.3 % / Redundancy: 6.2 % / CC1/2: 0.977 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.068 / Rrim(I) all: 0.172 / Net I/σ(I): 6.5
Reflection shellResolution: 1.494→1.535 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / Num. unique obs: 3941 / CC1/2: 0.106 / Rpim(I) all: 0.387 / Rrim(I) all: 0.965 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROC1.0.5data processing
STARANISOdata scaling
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.494→19.244 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.238 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2043 3979 5.048 %
Rwork0.1798 74849 -
all0.181 --
obs-78828 91.009 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0.003 Å2-0 Å2
2---0.005 Å20 Å2
3---0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.494→19.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 44 275 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163115
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.6644488
X-RAY DIFFRACTIONr_angle_other_deg0.6811.5657111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.056543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10210494
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.69910147
X-RAY DIFFRACTIONr_chiral_restr0.1070.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined0.2380.2637
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22741
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21662
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2169
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.213
X-RAY DIFFRACTIONr_nbd_other0.3020.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1340.21
X-RAY DIFFRACTIONr_mcbond_it2.2671.7631643
X-RAY DIFFRACTIONr_mcbond_other2.2641.7631643
X-RAY DIFFRACTIONr_mcangle_it3.1613.1662052
X-RAY DIFFRACTIONr_mcangle_other3.163.1662053
X-RAY DIFFRACTIONr_scbond_it4.2222.1811655
X-RAY DIFFRACTIONr_scbond_other4.2212.181656
X-RAY DIFFRACTIONr_scangle_it6.0793.8112436
X-RAY DIFFRACTIONr_scangle_other6.0783.8112437
X-RAY DIFFRACTIONr_lrange_it6.75120.3343688
X-RAY DIFFRACTIONr_lrange_other6.74419.6523631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.494-1.5330.251470.24735010.24863660.9570.9557.30440.241
1.533-1.5740.2252340.22644560.22661940.9660.96875.71840.218
1.574-1.620.2122270.20546380.20559640.9720.97381.57280.193
1.62-1.6690.2622560.20248160.20558680.9570.97486.43490.189
1.669-1.7240.2132680.19649360.19756860.970.97591.5230.182
1.724-1.7840.2252510.19250340.19454450.9670.97797.06150.179
1.784-1.850.2232790.18549550.18753140.970.97998.49450.172
1.85-1.9250.1932710.17747610.17850920.9750.9898.82170.17
1.925-2.010.1972560.17346050.17548990.9770.98299.22430.17
2.01-2.1070.1862610.17243680.17346690.9790.98299.14330.175
2.107-2.2190.2042390.17341840.17544760.9770.98298.81590.179
2.219-2.3520.1962050.16739720.16942320.9760.98398.70040.18
2.352-2.5120.1851940.16536980.16639710.9780.98498.01060.184
2.512-2.7090.2222150.17533850.17837000.9720.98197.29730.202
2.709-2.9620.2011470.18531690.18634140.9760.97997.12950.218
2.962-3.3010.2441410.20329310.20531370.9620.97697.9280.242
3.301-3.7940.21340.17525390.17627450.9780.98497.37710.217
3.794-4.6020.1581140.14921610.1523500.9830.98796.80850.197
4.602-6.3290.198810.17716980.17818710.9850.98795.08280.237
6.329-19.2440.217590.19810420.19911570.9750.98295.15990.259

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