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- PDB-1t56: Crystal structure of TetR family repressor M. tuberculosis EthR -

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Basic information

Entry
Database: PDB / ID: 1t56
TitleCrystal structure of TetR family repressor M. tuberculosis EthR
ComponentsEthR repressor
KeywordsTRANSCRIPTION / helix-turn-helix / TetR family / dimer
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
1,4-DIETHYLENE DIOXIDE / HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsDover, L.G. / Corsino, P.E. / Daniels, I.R. / Cocklin, S.L. / Tatituri, V. / Besra, G.S. / Futterer, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the TetR/CamR Family Repressor Mycobacterium tuberculosis EthR Implicated in Ethionamide Resistance.
Authors: Dover, L.G. / Corsino, P.E. / Daniels, I.R. / Cocklin, S.L. / Tatituri, V. / Besra, G.S. / Futterer, K.
History
DepositionMay 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: EthR repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0504
Polymers23,7821
Non-polymers2683
Water2,126118
1
A: EthR repressor
hetero molecules

A: EthR repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1008
Polymers47,5632
Non-polymers5376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4330 Å2
ΔGint-2 kcal/mol
Surface area17600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.500, 121.500, 33.500
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-355-

HOH

21A-359-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis parallel to a + b: y, x, -z.

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Components

#1: Protein EthR repressor


Mass: 23781.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P96222, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: ammonium sulphate, 1,4-dioxane, glycerol, 1-(4-morpholino)ethanesulfonic acid, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 27776 / Num. obs: 27776 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.296 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.926 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1439 5.1 %RANDOM
Rwork0.20768 ---
all0.2083 27776 --
obs0.20836 26838 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 18 118 1623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211535
X-RAY DIFFRACTIONr_bond_other_d0.0020.021408
X-RAY DIFFRACTIONr_angle_refined_deg0.9241.9472089
X-RAY DIFFRACTIONr_angle_other_deg0.77333245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9375192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021717
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02319
X-RAY DIFFRACTIONr_nbd_refined0.2160.2376
X-RAY DIFFRACTIONr_nbd_other0.220.21535
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.2872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4050.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5241.5963
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00221544
X-RAY DIFFRACTIONr_scbond_it1.5223572
X-RAY DIFFRACTIONr_scangle_it2.5694.5545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.236 211
Rwork0.21 3831
Refinement TLS params.Method: refined / Origin x: 34.2691 Å / Origin y: 16.8321 Å / Origin z: 16.3899 Å
111213212223313233
T0.0154 Å20.0124 Å20.0111 Å2-0.0312 Å20.0168 Å2--0.011 Å2
L1.9253 °20.1857 °2-0.0215 °2-0.1958 °2-0.1657 °2--0.4883 °2
S0.0503 Å °0.0124 Å °0.0329 Å °-0.0454 Å °-0.0608 Å °-0.046 Å °0.0027 Å °0.1385 Å °0.0105 Å °

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