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- PDB-6hs1: EthR2 in complex with compound 9 (BDM76060) -

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Basic information

Entry
Database: PDB / ID: 6hs1
TitleEthR2 in complex with compound 9 (BDM76060)
ComponentsProbable transcriptional regulatory protein
KeywordsDNA BINDING PROTEIN / HELIX-TURN-HELIX / TETR-FAMILY / COMPLEX / INHIBITOR / DRUG DESIGN / TUBERCULOSIS / ETHIONAMIDE
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-GO5 / Probable transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWintjens, R. / Wohlkonig, A. / Tanina, A.
CitationJournal: Eur J Med Chem / Year: 2019
Title: A fragment-based approach towards the discovery of N-substituted tropinones as inhibitors of Mycobacterium tuberculosis transcriptional regulator EthR2.
Authors: Prevet, H. / Moune, M. / Tanina, A. / Kemmer, C. / Herledan, A. / Frita, R. / Wohlkonig, A. / Bourotte, M. / Villemagne, B. / Leroux, F. / Gitzinger, M. / Baulard, A.R. / Deprez, B. / ...Authors: Prevet, H. / Moune, M. / Tanina, A. / Kemmer, C. / Herledan, A. / Frita, R. / Wohlkonig, A. / Bourotte, M. / Villemagne, B. / Leroux, F. / Gitzinger, M. / Baulard, A.R. / Deprez, B. / Wintjens, R. / Willand, N. / Flipo, M.
History
DepositionSep 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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)48,5233
Polymers48,2452
Non-polymers2781
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-29 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.460, 74.010, 91.650
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: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 11 - 200 / Label seq-ID: 31 - 220

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

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Components

#1: Protein Probable transcriptional regulatory protein


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)
Gene: Rv0078 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O53623
#2: Chemical ChemComp-GO5 / (1~{R},5~{S})-9-[2-(4-chlorophenyl)ethyl]-9-azabicyclo[3.3.1]nonan-3-one


Mass: 277.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20ClNO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M ammonium chloride, 0.1M MES, 20% (W/V) PEG600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→57.58 Å / Num. obs: 45240 / % possible obs: 99 % / Redundancy: 4.6 % / Rrim(I) all: 0.056 / Net I/σ(I): 14.25
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.17 / Num. unique obs: 2215 / Rrim(I) all: 0.827 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Cootmodel building
XDSdata scaling
MOLREPphasing
autoPROCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7O

5n7o


Resolution: 1.69→57.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.07 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24885 2271 5 %RANDOM
Rwork0.2175 ---
obs0.21906 42969 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.646 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.69→57.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 19 85 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132976
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172912
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6554037
X-RAY DIFFRACTIONr_angle_other_deg1.5341.596658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8625382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.21619.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05515492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051540
X-RAY DIFFRACTIONr_chiral_restr0.0770.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
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_it2.483.0081535
X-RAY DIFFRACTIONr_mcbond_other2.4463.0061532
X-RAY DIFFRACTIONr_mcangle_it3.2524.5071914
X-RAY DIFFRACTIONr_mcangle_other3.2214.5081914
X-RAY DIFFRACTIONr_scbond_it4.2523.6641441
X-RAY DIFFRACTIONr_scbond_other4.2513.6641442
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.55.2652124
X-RAY DIFFRACTIONr_long_range_B_refined7.63836.753356
X-RAY DIFFRACTIONr_long_range_B_other7.63736.7473357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5659 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.694→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 182 -
Rwork0.326 3095 -
obs--98.65 %

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