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- PDB-2vkv: TetR (BD) variant L17G with reverse phenotype -

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Basic information

Entry
Database: PDB / ID: 2vkv
TitleTetR (BD) variant L17G with reverse phenotype
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / DISORDER TO ORDER MECHANISM / ANTIBIOTIC RESISTANCE / HELIX-TURN-HELIX MOTIF / BACTERIAL REPRESSOR / ANHYDROTETRACYCLINE / METAL-BINDING / REVERSE PHENOTYPE / TETR / PLASMID / REPRESSOR / MAGNESIUM / DNA-BINDING
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
5A,6-ANHYDROTETRACYCLINE / Tetracycline repressor protein class B from transposon Tn10 / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsResch, M. / Striegl, H. / Henssler, E.M. / Sevvana, M. / Egerer-Sieber, C. / Schiltz, E. / Hillen, W. / Muller, Y.A.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: A Protein Functional Leap: How a Single Mutation Reverses the Function of the Transcription Regulator Tetr.
Authors: Resch, M. / Striegl, H. / Henssler, E.M. / Sevvana, M. / Egerer-Sieber, C. / Schiltz, E. / Hillen, W. / Muller, Y.A.
History
DepositionJan 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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, TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8254
Polymers23,3501
Non-polymers4753
Water2,990166
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6498
Polymers46,6992
Non-polymers9506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7050 Å2
ΔGint-46.9 kcal/mol
Surface area21350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.650, 54.460, 56.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D / TETRACYCLINE REPRESSOR BD VARIANT L17G


Mass: 23349.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-50,51-208 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-50 ARE FROM VARIANT B, RESIDUES 51-208 ARE FROM VARIANT D
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH610/LEU17GLYTETR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791 / References: UniProt: P04483, UniProt: P0ACT4
#2: Chemical ChemComp-TDC / 5A,6-ANHYDROTETRACYCLINE


Mass: 426.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 17 TO GLY

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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: 2.35 Å3/Da / Density % sol: 47.8 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.7
Details: 0.1 M TRIS-HCL (PH 8.7), 0.3 M MGCL2, 20 % PEG 4000, 3 % DIOXANE, AT 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 18, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→19.66 Å / Num. obs: 22843 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.2
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 8.84 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TCT

2tct


Resolution: 1.74→19.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.058 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2218 9.7 %RANDOM
Rwork0.175 ---
obs0.18 20625 100 %-
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 mean: 41.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.74→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 33 166 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211694
X-RAY DIFFRACTIONr_bond_other_d0.0010.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.992318
X-RAY DIFFRACTIONr_angle_other_deg0.89532776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.445219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59423.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31215289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7881516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
X-RAY DIFFRACTIONr_nbd_refined0.220.2397
X-RAY DIFFRACTIONr_nbd_other0.1820.21139
X-RAY DIFFRACTIONr_nbtor_refined0.180.2846
X-RAY DIFFRACTIONr_nbtor_other0.0850.2842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4231.51347
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62621646
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2063777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2894.5663
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.8 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.254 229
Rwork0.208 1936
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)
13.29173.30964.90274.52428.495317.9289-0.02130.22560.28410.6330.1720.75940.49981.1341-0.1507-0.01270.0015-0.09980.1349-0.0131-0.1945-21.32324.21693.3675
20.41240.1232-0.75960.71140.11051.91570.0085-0.0526-0.01070.0013-0.061-0.19320.05610.07330.05250.02610.0011-0.00880.04540.00040.0642-20.84532.2629-20.5885
30.53660.3295-0.13840.9039-0.55870.63960.0158-0.05170.0137-0.00650.0055-0.03730.01190.0128-0.02140.0442-0.0050.0070.0360.00550.0535-27.86373.801-20.4894
40.93231.328-0.48361.8952-0.66350.6658-0.01320.1026-0.1559-0.12150.0518-0.12610.09130.0061-0.03860.03690.0091-0.01210.0318-0.00740.0719-36.0467-10.1173-29.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 45
2X-RAY DIFFRACTION2A46 - 91
3X-RAY DIFFRACTION3A92 - 161
4X-RAY DIFFRACTION4A162 - 205

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