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- PDB-6sy4: TetR in complex with the TetR-binding RNA-aptamer K1 -

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Basic information

Entry
Database: PDB / ID: 6sy4
TitleTetR in complex with the TetR-binding RNA-aptamer K1
Components
  • TetR-binding aptamer K1 (43-MER)
  • Tetracycline repressor protein class B from transposon Tn10
KeywordsDNA BINDING PROTEIN / TetR / Complex / Aptamer / Transcriptional regulator
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
RNA / RNA (> 10) / Tetracycline repressor protein class B from transposon Tn10
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.695 Å
AuthorsGrau, F.C. / Muller, Y.A. / Suess, B. / Groher, F. / Jaeger, J.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex.
Authors: Grau, F.C. / Jaeger, J. / Groher, F. / Suess, B. / Muller, Y.A.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Tetracycline repressor protein class B from transposon Tn10
B: Tetracycline repressor protein class B from transposon Tn10
C: TetR-binding aptamer K1 (43-MER)


Theoretical massNumber of molelcules
Total (without water)61,0993
Polymers61,0993
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-43 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.027, 96.027, 163.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 41 or resid 43...
21(chain B and (resid 4 through 41 or resid 43...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 41 or resid 43...A4 - 41
121(chain A and (resid 4 through 41 or resid 43...A43 - 103
131(chain A and (resid 4 through 41 or resid 43...A105 - 6
141(chain A and (resid 4 through 41 or resid 43...A3 - 202
151(chain A and (resid 4 through 41 or resid 43...A123 - 150
161(chain A and (resid 4 through 41 or resid 43...A152 - 154
171(chain A and (resid 4 through 41 or resid 43...A181 - 187
181(chain A and (resid 4 through 41 or resid 43...A189 - 194
191(chain A and (resid 4 through 41 or resid 43...A196 - 202
211(chain B and (resid 4 through 41 or resid 43...B4 - 41
221(chain B and (resid 4 through 41 or resid 43...B43 - 103
231(chain B and (resid 4 through 41 or resid 43...B3 - 202
241(chain B and (resid 4 through 41 or resid 43...B3 - 202
251(chain B and (resid 4 through 41 or resid 43...B108 - 121
261(chain B and (resid 4 through 41 or resid 43...B152 - 154
271(chain B and (resid 4 through 41 or resid 43...B1
281(chain B and (resid 4 through 41 or resid 43...B196 - 202

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Components

#1: Protein Tetracycline repressor protein class B from transposon Tn10


Mass: 23531.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04483
#2: RNA chain TetR-binding aptamer K1 (43-MER)


Mass: 14035.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.14 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 4% v/v Tacsimate pH 6.0, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 1, 2017
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.695→15.764 Å / Num. obs: 21786 / % possible obs: 99.9 % / Redundancy: 25.993 % / Biso Wilson estimate: 75.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.196 / Rrim(I) all: 0.2 / Χ2: 0.969 / Net I/σ(I): 17.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.7725.3563.6970.9239987157715770.3373.772100
2.77-2.8422.9322.8171.235178153415340.4632.881100
2.84-2.9226.6752.3871.5439773149114910.5792.433100
2.92-3.0128.0361.722.341185146914690.7441.751100
3.01-3.1127.7991.3392.9839252141414120.851.36399.9
3.11-3.2227.6780.8974.5737780136513650.9330.914100
3.22-3.3427.430.6176.6435933131013100.9640.628100
3.34-3.4827.0810.4429.1835070129512950.9840.45100
3.48-3.6326.9040.33112.1532554121012100.990.337100
3.63-3.8126.2030.23516.6630867117811780.9950.24100
3.81-4.0224.5720.18919.9227865113411340.9960.193100
4.02-4.2622.3390.15622.6823769106410640.9970.159100
4.26-4.5627.5550.12230.6627803101010090.9990.12499.9
4.56-4.9227.1530.10634.95254429379370.9990.108100
4.92-5.3926.8560.09338.82236338808800.9990.095100
5.39-6.0325.9460.09936.19206537977960.9990.10199.9
6.03-6.9624.4430.08640.03174287137130.9990.088100
6.96-8.5220.9850.0559.761299061961910.051100
8.52-12.0526.1410.02797.741296649649610.027100
12.05-15.76420.7340.02674.55615830429710.02697.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS7

2ns7


Resolution: 2.695→15.764 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.246 1098 5.07 %
Rwork0.2012 --
obs0.2036 21641 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 187.53 Å2 / Biso mean: 80.4598 Å2 / Biso min: 39.26 Å2
Refinement stepCycle: final / Resolution: 2.695→15.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 785 0 19 3701
Biso mean---65.45 -
Num. residues----401
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A954X-RAY DIFFRACTION9.058TORSIONAL
12B954X-RAY DIFFRACTION9.058TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6954-2.81740.33811410.30852519
2.8174-2.96510.331330.29852515
2.9651-3.14940.32011440.2562509
3.1494-3.39040.32341420.22852516
3.3904-3.72750.28551290.19832563
3.7275-4.25750.22081270.17742578
4.2575-5.32940.23931250.1772625
5.3294-15.7640.19881570.18842718
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)
10.6625-0.29680.56890.728-0.81151.1755-0.02030.0621-0.1215-0.0741-0.04810.16680.0221-0.17720.00050.37080.02630.01140.65210.00850.5711-9.4459-33.2153-37.0564
20.92030.0663-0.35061.2839-0.70051.4487-0.0302-0.12220.17450.2229-0.1167-0.1115-0.41780.1866-0.00010.4505-0.0895-0.09910.5957-0.00490.55778.8428-21.3282-31.4186
3-0.0071-0.25470.46031.9026-1.24381.07610.08580.23070.1115-0.3243-0.117-0.2593-0.2090.10020.07820.68110.05870.01930.94680.17560.72430.5311-13.2103-68.3485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 202)A3 - 202
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 202)B3 - 202
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 41)C4 - 41

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