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- PDB-6fts: TETR(D) N82A MUTANT IN COMPLEX WITH PEG4 -

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Basic information

Entry
Database: PDB / ID: 6fts
TitleTETR(D) N82A MUTANT IN COMPLEX WITH PEG4
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
Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)23,5104
Polymers23,2451
Non-polymers2653
Water1,78399
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0218
Polymers46,4912
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6080 Å2
ΔGint-58 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.779, 68.779, 180.140
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-490-

HOH

21A-493-

HOH

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Components

#1: Protein Tetracycline repressor protein class D


Mass: 23245.309 Da / Num. of mol.: 1
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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Precipitant: 2M (NH4)2SO4, 6% PEG400, 0.1M Tris pH8.5. 19.65mg/ml Protein, 2mM Tetracycline, 3M MgCl2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 7, 2007
RadiationMonochromator: osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→34.39 Å / Num. obs: 14920 / % possible obs: 98.7 % / Redundancy: 9.55 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1360 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRT, 2TCT

2trt

2tct


Resolution: 2→34.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.535 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27236 1016 6.9 %RANDOM
Rwork0.22213 ---
obs0.22579 13663 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2---0.16 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 2→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 15 99 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191662
X-RAY DIFFRACTIONr_bond_other_d0.0010.021616
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9712251
X-RAY DIFFRACTIONr_angle_other_deg0.83533697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9735208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70123.29382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01115290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.591517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
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_it3.1753.208820
X-RAY DIFFRACTIONr_mcbond_other3.1753.208819
X-RAY DIFFRACTIONr_mcangle_it4.8764.781032
X-RAY DIFFRACTIONr_mcangle_other4.8744.781033
X-RAY DIFFRACTIONr_scbond_it3.1023.531842
X-RAY DIFFRACTIONr_scbond_other3.1023.531842
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9945.2081220
X-RAY DIFFRACTIONr_long_range_B_refined8.27325.1692015
X-RAY DIFFRACTIONr_long_range_B_other8.24725.0491992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 81 -
Rwork0.317 924 -
obs--89.57 %
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)
11.9391-0.19262.86530.0775-0.19494.3820.02070.1591-0.01790.0449-0.01210.01980.10360.1985-0.00860.0533-0.0044-0.01450.2541-0.04940.110619.104128.432813.979
20.96080.4710.3320.25240.33851.71120.2640.16920.03040.13670.0681-0.01810.0133-0.1004-0.33210.18860.10810.0380.14120.00850.115325.402332.732140.3107
312.538-3.2756-0.44496.58361.2720.24930.1115-0.29460.6295-0.2257-0.1059-0.095-0.0396-0.023-0.00550.10090.0827-0.01790.0798-0.03370.129850.11620.123937.6239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 103
3X-RAY DIFFRACTION2A106 - 154
4X-RAY DIFFRACTION2A180 - 208
5X-RAY DIFFRACTION2A1209
6X-RAY DIFFRACTION3A168 - 179

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