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- PDB-6qjw: TetR(D) T103A mutant in complex with 7-chlortetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 6qjw
TitleTetR(D) T103A mutant in complex with 7-chlortetracycline 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
7-CHLOROTETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)23,9398
Polymers23,2581
Non-polymers6807
Water1,964109
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,87816
Polymers46,5172
Non-polymers1,36114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area8340 Å2
ΔGint-152 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.138, 68.138, 180.917
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-440-

HOH

21A-507-

HOH

31A-509-

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-CTC / 7-CHLOROTETRACYCLINE


Mass: 478.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN2O8
#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.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Precipitant: 30%PEG 400, 0.1M MES pH 6.5, 60 mM MgCl2. Protein: 12.15 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, 4mM 7ClTc, 3M MgCl2. Protein/precipitant 1/1

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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: Oct 17, 2014 / 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: 2.1→34.09 Å / Num. obs: 12896 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.85 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.13 / Χ2: 0.97 / Net I/σ(I): 6.85
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.487 / Num. unique obs: 1245 / Χ2: 1.23 / % possible all: 100

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Processing

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

2tct


Resolution: 2.1→34.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.474 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.247 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29024 1266 9.9 %RANDOM
Rwork0.21988 ---
obs0.22694 11569 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0 Å2-0 Å2
2--0.48 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.1→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 39 109 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171572
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.652296
X-RAY DIFFRACTIONr_angle_other_deg1.4321.5783628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.595206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9220.971103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33715292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0851516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021924
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02364
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_it1.7022.285815
X-RAY DIFFRACTIONr_mcbond_other1.7012.285814
X-RAY DIFFRACTIONr_mcangle_it2.6013.4081024
X-RAY DIFFRACTIONr_mcangle_other2.63.4081025
X-RAY DIFFRACTIONr_scbond_it1.9292.549868
X-RAY DIFFRACTIONr_scbond_other1.9232.543860
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1463.7511273
X-RAY DIFFRACTIONr_long_range_B_refined5.42427.632043
X-RAY DIFFRACTIONr_long_range_B_other5.25427.5012020
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 86 -
Rwork0.253 826 -
obs--99.67 %
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)
10.7843-0.1491.20940.0921-0.06642.322-0.0017-0.00790.01330.00890.0449-0.03360.03650.0204-0.04330.0489-0.0360.01050.1484-0.04010.055919.051328.26413.9957
20.58170.190.20010.08210.10570.37170.10680.12-0.02660.05460.0145-0.00640.00850.0057-0.12130.12820.06680.00430.1035-0.03430.068227.835531.085539.6568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 63
2X-RAY DIFFRACTION1A303 - 306
3X-RAY DIFFRACTION2A64 - 208
4X-RAY DIFFRACTION2A301 - 302

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