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- PDB-3fk7: Crystal structure of TetR triple mutant (H64K, S135L, S138I) in c... -

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Basic information

Entry
Database: PDB / ID: 3fk7
TitleCrystal structure of TetR triple mutant (H64K, S135L, S138I) in complex with 4-ddma-atc
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


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 / 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
Chem-4DM / 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 / FOURIER SYNTHESIS / Resolution: 2.06 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 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7136
Polymers46,8982
Non-polymers8154
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-60 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.220, 59.380, 63.780
Angle α, β, γ (deg.)90.000, 97.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-286-

HOH

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-4DM / (4aS,12aS)-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-1,4,4a,5,12,12a-hexahydrotetracene-2-carboxamide


Mass: 383.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H17NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
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: 0.9082 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9082 Å / Relative weight: 1
ReflectionResolution: 2.06→42.22 Å / Num. all: 30027 / Num. obs: 29597 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.06→2.19 Å / Rmerge(I) obs: 0.398 / Num. unique all: 4994 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3FK6

3fk6


Resolution: 2.06→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.947 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2368 8 %RANDOM
Rwork0.203 ---
obs0.208 29594 100 %-
all-29594 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.69 Å2 / Biso mean: 36.79 Å2 / Biso min: 13.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.52 Å2
2--0.63 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 58 225 3463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223299
X-RAY DIFFRACTIONr_bond_other_d0.0010.022228
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9964482
X-RAY DIFFRACTIONr_angle_other_deg0.88835420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.225401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34523.938160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59615583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6081528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
X-RAY DIFFRACTIONr_nbd_refined0.2170.2832
X-RAY DIFFRACTIONr_nbd_other0.180.22351
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21637
X-RAY DIFFRACTIONr_nbtor_other0.0880.21641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.212
X-RAY DIFFRACTIONr_mcbond_it1.24422602
X-RAY DIFFRACTIONr_mcbond_other0.212808
X-RAY DIFFRACTIONr_mcangle_it1.4062.53169
X-RAY DIFFRACTIONr_scbond_it2.12641561
X-RAY DIFFRACTIONr_scangle_it3.16361309
LS refinement shellResolution: 2.064→2.175 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 326 -
Rwork0.267 3750 -
all-4076 -
obs--100 %

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