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- PDB-3fk6: Crystal structure of TetR triple mutant (H64K, S135L, S138I) -

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Basic information

Entry
Database: PDB / ID: 3fk6
TitleCrystal structure of TetR triple mutant (H64K, S135L, S138I)
ComponentsTetracycline repressor protein class B from transposon Tn10, Tetracycline repressor protein class D
KeywordsTRANSCRIPTION / Tetracycline repressor / bacterial transcription regulation / altered inducer specificity / 4-de-dimethylamino-anhydrotetracycline / Antibiotic resistance / DNA-binding / Magnesium / Metal-binding / Repressor / Transcription regulation / Transposable element
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 B from transposon Tn10 / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKlieber, M.A. / Scholz, O. / Lochner, S. / Gmeiner, P. / Hillen, W. / Muller, Y.A.
CitationJournal: Febs J. / Year: 2009
Title: Structural origins for selectivity and specificity in an engineered bacterial repressor-inducer pair.
Authors: Klieber, M.A. / Scholz, O. / Lochner, S. / Gmeiner, P. / Hillen, W. / Muller, Y.A.
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tetracycline repressor protein class B from transposon Tn10, Tetracycline repressor protein class D
B: Tetracycline repressor protein class B from transposon Tn10, Tetracycline repressor protein class D


Theoretical massNumber of molelcules
Total (without water)46,8982
Polymers46,8982
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-39 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.350, 58.060, 62.620
Angle α, β, γ (deg.)90.000, 96.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23448.801 Da / Num. of mol.: 2
Fragment: DNA-binding domain (residues 1-50) and the effector-binding domain (residues 51-208)
Mutation: H64K, S135L, S138I
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF DNA-BINDING DOMAIN (RESIDUES 1-50) FROM TETR VARIANT B AND THE EFFECTOR-BINDING DOMAIN (RESIDUES 51-208) FROM TETR VARIANT D
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tetR / Plasmid: pWH610 / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P04483, UniProt: P0ACT4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FUSION PROTEIN OF DNA-BINDING DOMAIN (RESIDUES 1-50) FROM TETR VARIANT B AND THE EFFECTOR- ...THE FUSION PROTEIN OF DNA-BINDING DOMAIN (RESIDUES 1-50) FROM TETR VARIANT B AND THE EFFECTOR-BINDING DOMAIN (RESIDUES 51-208) FROM TETR VARIANT D

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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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M dipotassium hydrogen phosphate, 200mM sodium chloride, 50mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 26513 / Num. obs: 24749 / % possible obs: 93.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.1→2.25 Å / Rmerge(I) obs: 0.371 / Num. unique all: 4925 / % possible all: 95.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 2.1→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1995 7.5 %RANDOM
Rwork0.216 ---
all-24749 --
obs-24749 93.4 %-
Solvent computationBsol: 51.836 Å2
Displacement parametersBiso max: 87.66 Å2 / Biso mean: 43.256 Å2 / Biso min: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.575 Å20 Å20.584 Å2
2---5.831 Å20 Å2
3---3.256 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3093 0 0 116 3209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.069
X-RAY DIFFRACTIONc_mcbond_it1.5051.5
X-RAY DIFFRACTIONc_scbond_it2.2752
X-RAY DIFFRACTIONc_mcangle_it2.3882
X-RAY DIFFRACTIONc_scangle_it3.4642.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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