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- PDB-5icj: Crystal structure of the Mycobacterium tuberculosis transcription... -

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Basic information

Entry
Database: PDB / ID: 5icj
TitleCrystal structure of the Mycobacterium tuberculosis transcriptional repressor EthR2 in complex with BDM41420
ComponentsProbable transcriptional regulatory protein
KeywordsTRANSCRIPTION / HELIX-TURN-HELIX DNA BINDING PROTEIN / TETR FAMILY / REGULATORY REPRESSOR / INHIBITOR / TRANSCRIPTION REPRESSOR-INHIBITOR COMPLEX
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: 2.4 Å
AuthorsWohlkonig, A. / Remaut, H. / Tanina, A. / Meyer, F. / Willand, N. / Baulard, A.R. / Wintjens, R.
Citation
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.
#1: 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.
History
DepositionFeb 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 10, 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
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.800, 74.210, 88.140
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: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 12 - 201 / Label seq-ID: 32 - 221

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.787281, 0.5783, -0.213911), (0.570618, -0.814779, -0.102613), (-0.233632, -0.041276, -0.971449)-8.42068, 19.23407, -22.96836

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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
Details: RESIDUE 1-20 ARE THE PURIFICATION TAG / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0078, LH57_00450 / Plasmid: pET15b / Details (production host): CLONAGE SITES: NdeI-BamH1 / Production host: Escherichia coli BL21(DE3) (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 / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 200 mM NaCl, 200 mM Na citrate pH 4.2 and 15% polyethylene glycol monomethylether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979338 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 15854 / % possible obs: 99.8 % / Redundancy: 12.83 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Net I/σ(I): 19.21
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 2.81 / CC1/2: 0.849 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
MOLREP11.2.05phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICI

5ici
PDB Unreleased entry


Resolution: 2.4→37.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.119 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26015 793 5 %RANDOM
Rwork0.21182 ---
obs0.21422 15053 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.358 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 48 3 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192874
X-RAY DIFFRACTIONr_bond_other_d0.0020.022802
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9843918
X-RAY DIFFRACTIONr_angle_other_deg0.98936370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9665373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01222.991117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6915440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2471530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02635
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_it3.6374.8151505
X-RAY DIFFRACTIONr_mcbond_other3.64.8141500
X-RAY DIFFRACTIONr_mcangle_it5.1527.2171873
X-RAY DIFFRACTIONr_mcangle_other5.1527.2191872
X-RAY DIFFRACTIONr_scbond_it4.3935.2341369
X-RAY DIFFRACTIONr_scbond_other4.3925.2341370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5357.7082046
X-RAY DIFFRACTIONr_long_range_B_refined8.34859.243187
X-RAY DIFFRACTIONr_long_range_B_other8.34659.2323188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10858 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 55 -
Rwork0.312 1047 -
obs--98.48 %

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