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- PDB-6rbl: TETR(D) E147A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM -

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Basic information

Entry
Database: PDB / ID: 6rbl
TitleTETR(D) E147A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM
ComponentsTetracycline repressor protein class D
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / 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 / DNA-binding HTH domain, TetR-type ...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-DXT / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionApr 10, 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.journal_abbrev / _citation.journal_id_CSD ..._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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)23,9129
Polymers23,2301
Non-polymers6818
Water2,900161
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,82418
Polymers46,4612
Non-polymers1,36316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area8690 Å2
ΔGint-147 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 68.300, 179.400
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-308-

CL

21A-499-

HOH

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Components

#1: Protein Tetracycline repressor protein class D


Mass: 23230.299 Da / Num. of mol.: 1 / Mutation: A2S, E147A
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-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE / Doxycycline


Mass: 444.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O8 / Feature type: SUBJECT OF INVESTIGATION / 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Precipitant: 2.0M (NH4)2SO4, 3% PEG 400, 0.1M MES pH 6.5, Protein: 0.1mL protein, 0.1,L 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris pH8.0, 1/3 protein/precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Apr 18, 2007 / Details: mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→34.17 Å / Num. obs: 17126 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1617 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FPL

6fpl


Resolution: 1.9→34.17 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.102 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1306 7.8 %RANDOM
Rwork0.20941 ---
obs0.21242 15434 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å20 Å2
2--0.28 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.9→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 39 161 1801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131690
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171578
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.6482302
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5753638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90921.1100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3711515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
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_it1.0841.453825
X-RAY DIFFRACTIONr_mcbond_other1.0841.453824
X-RAY DIFFRACTIONr_mcangle_it1.8182.1631033
X-RAY DIFFRACTIONr_mcangle_other1.8172.1641034
X-RAY DIFFRACTIONr_scbond_it1.231.552865
X-RAY DIFFRACTIONr_scbond_other1.2351.555857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9712.2811270
X-RAY DIFFRACTIONr_long_range_B_refined3.44117.3022024
X-RAY DIFFRACTIONr_long_range_B_other3.35417.1381991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 91 -
Rwork0.44 1056 -
obs--91.69 %
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)
11.1651-0.56681.9170.802-0.1984.21030.00320.08110.0501-0.06-0.037-0.028-0.04420.13470.03390.0601-0.0119-0.01740.0797-0.01220.07118.859128.259413.743
21.7061-0.04370.21361.39420.60032.73690.03030.01760.011-0.02610.02040.0202-0.06910.0731-0.05070.004-0.0036-0.00130.00560.00480.012924.945432.652439.4282
39.8083-0.1397-1.96722.31810.71441.5895-0.05660.6399-0.0326-0.3269-0.04090.27770.2875-0.09810.09750.21860.0213-0.0180.12960.00070.110750.001120.519735.9956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 63
2X-RAY DIFFRACTION2A64 - 156
3X-RAY DIFFRACTION2A182 - 208
4X-RAY DIFFRACTION2A301 - 302
5X-RAY DIFFRACTION3A165 - 181

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