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- PDB-5n7o: EthR2 in complex with SMARt-420 compound -

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Basic information

Entry
Database: PDB / ID: 5n7o
TitleEthR2 in complex with SMARt-420 compound
ComponentsProbable transcriptional regulatory protein
KeywordsTRANSCRIPTION / Repressor / complex / inhibitor
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Chem-69Y / Probable transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWohlkonig, A. / Wintjens, R.
Citation
Journal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural analysis of the interaction between spiroisoxazoline SMARt-420 and the Mycobacterium tuberculosis repressor EthR2.
Authors: Wohlkonig, A. / Remaut, H. / Moune, M. / Tanina, A. / Meyer, F. / Desroses, M. / Steyaert, J. / Willand, N. / Baulard, A.R. / Wintjens, R.
#1: Journal: Science / Year: 2017
Title: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420
Authors: Blondiaux, N. / Moune, M. / Desroses, M. / Frita, R. / Flipo, M. / Mathys, V. / Soetaert, K. / Kiass, M. / Delorme, V. / Djaout, K. / Trebosc, V. / Kemmer, C. / Wintjens, R. / Wohlkonig, A. ...Authors: Blondiaux, N. / Moune, M. / Desroses, M. / Frita, R. / Flipo, M. / Mathys, V. / Soetaert, K. / Kiass, M. / Delorme, V. / Djaout, K. / Trebosc, V. / Kemmer, C. / Wintjens, R. / Wohlkonig, A. / Antoine, R. / Huot, L. / Hot, D. / Coscolla, M. / Feldmann, J. / Gagneux, S. / Locht, C. / Brodin, P. / Gitzinger, M. / Deprez, B. / Willand, N. / Baulard, A.R.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulatory protein
B: Probable transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9264
Polymers48,2452
Non-polymers6812
Water43224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-29 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 74.290, 91.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 11 - 201 / Label seq-ID: 31 - 221

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable transcriptional regulatory protein / TetR family transcriptional regulator


Mass: 24122.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0078, LH57_00450 / Plasmid: pET15b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O53623
#2: Chemical ChemComp-69Y / 4,4,4-trifluoro-1-(3-phenyl-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl)butan-1-one


Mass: 340.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19F3N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M NaCl, 0.2 M Na citrate pH 4.2 and 15% PEG-MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→60 Å / Num. obs: 18592 / % possible obs: 98.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.998 / Rsym value: 0.118 / Net I/σ(I): 20.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2925 / CC1/2: 0.97 / Rsym value: 0.52 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSVERSION Oct 15, 2015data reduction
XDSVERSION Oct 15, 2015data scaling
MOLREPVersion 11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N1I

5n1i


Resolution: 2.3→57.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.282 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24764 927 5 %RANDOM
Rwork0.21487 ---
obs0.21653 17607 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.571 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→57.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 48 24 2968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192988
X-RAY DIFFRACTIONr_bond_other_d0.0020.022964
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9844058
X-RAY DIFFRACTIONr_angle_other_deg1.02636742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.025380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80322.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65615488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5261540
X-RAY DIFFRACTIONr_chiral_restr0.0960.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9163.2931530
X-RAY DIFFRACTIONr_mcbond_other2.8773.2921525
X-RAY DIFFRACTIONr_mcangle_it4.2524.9251906
X-RAY DIFFRACTIONr_mcangle_other4.2524.9291905
X-RAY DIFFRACTIONr_scbond_it4.2743.9421458
X-RAY DIFFRACTIONr_scbond_other4.2733.9411459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7885.6662153
X-RAY DIFFRACTIONr_long_range_B_refined8.43140.0473310
X-RAY DIFFRACTIONr_long_range_B_other8.43440.023307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11398 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 68 -
Rwork0.247 1285 -
obs--100 %

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