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- PDB-6fpl: TETR(D) E147A MUTANT IN COMPLEX WITH TETRACYCLINE AND MAGNESIUM -

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Basic information

Entry
Database: PDB / ID: 6fpl
TitleTETR(D) E147A MUTANT IN COMPLEX WITH TETRACYCLINE 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
TETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 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
DepositionFeb 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 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 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _refine_hist.d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water1,71195
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 area8850 Å2
ΔGint-161 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.020, 68.020, 179.030
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-429-

HOH

21A-495-

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-TAC / TETRACYCLINE


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


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 44.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Precipitant 0.1M Na-citrat, 0.8M Li2SO4, 0.5M (NH4)2SO4, 0.1mL Protein (10.19mg/ml, 0.1M MES pH 6.5) + 0.1mL 2mM Tc + 0.001mL 3M MgCl2 1:4 Precipitant/Protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.602→63.59 Å / Num. obs: 28147 / % possible obs: 94.5 % / Redundancy: 17.66 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 31.95
Reflection shellResolution: 1.602→1.644 Å / Num. unique obs: 1959 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRT

2trt


Resolution: 1.602→63.59 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.638 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22093 1318 5 %RANDOM
Rwork0.18604 ---
obs0.18772 25266 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.784 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å2-0 Å20 Å2
2--1.65 Å20 Å2
3----3.3 Å2
Refinement stepCycle: 1 / Resolution: 1.602→63.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 39 95 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191677
X-RAY DIFFRACTIONr_bond_other_d0.0010.021625
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9922287
X-RAY DIFFRACTIONr_angle_other_deg0.93933709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05823.45781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72715289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.121516
X-RAY DIFFRACTIONr_chiral_restr0.1460.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
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_it1.9872.386815
X-RAY DIFFRACTIONr_mcbond_other1.9812.386814
X-RAY DIFFRACTIONr_mcangle_it2.6473.5691024
X-RAY DIFFRACTIONr_mcangle_other2.6463.5691025
X-RAY DIFFRACTIONr_scbond_it2.9042.674861
X-RAY DIFFRACTIONr_scbond_other2.9032.674862
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2753.9031264
X-RAY DIFFRACTIONr_long_range_B_refined5.22619.552030
X-RAY DIFFRACTIONr_long_range_B_other5.18219.4111998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 97 -
Rwork0.274 1862 -
obs--95.98 %
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)
12.1642-0.69652.4130.6879-0.093.72220.00630.05360.03970.11490.0562-0.08180.19450.1222-0.06240.0839-0.0335-0.03360.127-0.02230.11518.94528.402813.5477
20.64410.27180.00310.15030.16021.1570.01510.04540.0185-0.00050.00930.04480.0351-0.045-0.02440.13120.0989-0.01960.0812-0.00710.122524.947532.44139.272
34.9463.7541.73232.85821.31260.6175-0.02680.1648-0.4925-0.0880.1334-0.35860.0290.0824-0.10660.3470.20070.07190.1404-0.00660.18350.530220.55135.6989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 45
2X-RAY DIFFRACTION1A46 - 64
3X-RAY DIFFRACTION1A1212 - 1216
4X-RAY DIFFRACTION2A65 - 93
5X-RAY DIFFRACTION2A101 - 106
6X-RAY DIFFRACTION2A107 - 123
7X-RAY DIFFRACTION2A94 - 100
8X-RAY DIFFRACTION2A124 - 155
9X-RAY DIFFRACTION2A182 - 208
10X-RAY DIFFRACTION2A1209 - 1211
11X-RAY DIFFRACTION3A165 - 181

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