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- PDB-6qjx: TetR(D) T103A mutant in complex with minocycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 6qjx
TitleTetR(D) T103A mutant in complex with minocycline and magnesium
ComponentsTetracycline repressor protein class D
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION
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 / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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-MIY / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHinrichs, W. / Palm, G.J. / Berndt, L. / Girbardt, B.
Citation
Journal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.
Authors: Palm, G.J. / Buchholz, I. / Werten, S. / Girbardt, B. / Berndt, L. / Delcea, M. / Hinrichs, W.
#1: Journal: FEBS J. / Year: 2016
Title: Modular organisation of inducer recognition and allostery in the tetracycline repressor.
Authors: Werten, S. / Schneider, J. / Palm, G.J. / Hinrichs, W.
History
DepositionJan 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8827
Polymers23,2581
Non-polymers6246
Water73941
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,76414
Polymers46,5172
Non-polymers1,24712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area7650 Å2
ΔGint-129 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.810, 67.810, 180.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

#1: Protein Tetracycline repressor protein class D


Mass: 23258.307 Da / Num. of mol.: 1 / Mutation: A2S, T103A
Source method: isolated from a genetically manipulated source
Details: RA1-plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Plasmid: pwH1950 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACT4
#2: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Precipitant: 0.1 M MES pH 6.5, 24% PEG 400, 70 mM MgCl2. Protein: 14.55 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, with 2mM MinoTc, 0.38 uL 3M MgCl2. Precipitant/protein 1/4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2011 / Details: NULL
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→57 Å / Num. obs: 11944 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.85 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.15
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.54 / Num. unique obs: 1928 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TCT

2tct


Resolution: 2.1→42.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.993 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28008 1148 9.6 %RANDOM
Rwork0.22775 ---
obs0.23274 10762 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.701 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å2-0 Å20 Å2
2--3.27 Å2-0 Å2
3----6.54 Å2
Refinement stepCycle: 1 / Resolution: 2.1→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 38 41 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131665
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171541
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.7052272
X-RAY DIFFRACTIONr_angle_other_deg1.4111.6143548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85721.45896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28315280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8941515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
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_it2.9653.786784
X-RAY DIFFRACTIONr_mcbond_other2.9573.786783
X-RAY DIFFRACTIONr_mcangle_it4.5035.67979
X-RAY DIFFRACTIONr_mcangle_other4.5015.67980
X-RAY DIFFRACTIONr_scbond_it2.7374.147879
X-RAY DIFFRACTIONr_scbond_other2.7354.147880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3326.1161293
X-RAY DIFFRACTIONr_long_range_B_refined7.09445.7431977
X-RAY DIFFRACTIONr_long_range_B_other7.09145.7211973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 85 -
Rwork0.401 769 -
obs--93.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8486-0.21012.5520.18550.02324.1442-0.02380.05110.12950.09430.0121-0.08760.15920.06390.01170.0666-0.0357-0.03150.17750.0150.221418.915328.156413.7334
20.90910.65210.59060.48490.21223.2590.09250.13160.10410.08820.10230.1071-0.1064-0.1147-0.19490.15490.13510.03510.13110.00760.26724.673932.600640.2327
312.7825-2.4801-1.05610.50510.22960.1394-0.03190.34030.5050.0728-0.0053-0.09320.07710.02510.03720.21780.170.00590.1663-0.00340.241149.862819.894837.1729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 45
2X-RAY DIFFRACTION1A46 - 63
3X-RAY DIFFRACTION1A303 - 306
4X-RAY DIFFRACTION2A64 - 153
5X-RAY DIFFRACTION2A180 - 208
6X-RAY DIFFRACTION2A301 - 302
7X-RAY DIFFRACTION3A166 - 179

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