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- PDB-3o8g: EthR from Mycobacterium tuberculosis in complex with compound BDM14801 -

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Basic information

Entry
Database: PDB / ID: 3o8g
TitleEthR from Mycobacterium tuberculosis in complex with compound BDM14801
ComponentsTRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
KeywordsTRANSCRIPTION REPRESSOR/INHIBITOR / TetR-Family / Transcritptional regulatory repressor / inhibitor / DNA / DNA BINDING PROTEIN / TRANSCRIPTION REPRESSOR-INHIBITOR complex
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-O8G / HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWilland, N. / Desroses, M. / Toto, P. / Diri, B. / Lens, Z. / Villeret, V. / Rucktooa, P. / Locht, C. / Baulard, A. / Deprez, B.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: Exploring drug target flexibility using in situ click chemistry: application to a mycobacterial transcriptional regulator.
Authors: Willand, N. / Desroses, M. / Toto, P. / Dirie, B. / Lens, Z. / Villeret, V. / Rucktooa, P. / Locht, C. / Baulard, A. / Deprez, B.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2712
Polymers25,9531
Non-polymers3181
Water4,216234
1
A: TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
hetero molecules

A: TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5434
Polymers51,9062
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3160 Å2
ΔGint-21 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.010, 123.010, 33.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-218-

HOH

21A-402-

HOH

31A-416-

HOH

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR / Transcriptional regulator / TetR family


Mass: 25953.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, MT3970, Rv3855 / Production host: Escherichia coli (E. coli) / References: UniProt: P96222, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-O8G / 1-(azidoacetyl)-4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine / 2-azido-1-[4-(3-thiophen-2-yl-[1,2,4]oxadiazol-5-yl)-piperidin-1-yl]-ethanone


Mass: 318.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N6O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1mM Mes pH6.5, 1.5M Ammonium Sulfate and 10% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→32.69 Å / Num. all: 21076 / Num. obs: 20950 / % possible obs: 99.4 % / Observed criterion σ(F): 89526

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CCP4model building
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→32.69 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.796 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1047 5 %RANDOM
Rwork0.18213 ---
obs0.18408 19898 99.4 %-
all-21076 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 22 234 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9622135
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70423.78474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.841513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021209
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.2736
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.21080
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3060.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2581.51019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86521556
X-RAY DIFFRACTIONr_scbond_it2.633649
X-RAY DIFFRACTIONr_scangle_it3.8854.5579
X-RAY DIFFRACTIONr_rigid_bond_restr1.84131668
X-RAY DIFFRACTIONr_sphericity_free5.2433234
X-RAY DIFFRACTIONr_sphericity_bonded3.11131533
LS refinement shellResolution: 1.903→2.02 Å / Total num. of bins used: 20 /
Num. reflection% reflection
Rwork1395 -
obs13684 98.1 %

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