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- PDB-6rgx: TETR(D) N82A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM -

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Basic information

Entry
Database: PDB / ID: 6rgx
TitleTETR(D) N82A MUTANT IN COMPLEX WITH DOXYCYCLINE 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
Chem-DXT / TRIETHYLENE GLYCOL / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionApr 17, 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.journal_abbrev / _citation.journal_id_CSD ..._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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.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_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.ptnr2_auth_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetracycline repressor protein class D
B: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,65816
Polymers46,4912
Non-polymers1,16814
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, not exactly a homodimer, due to one empty ligand binding pocket
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-113 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.378, 68.378, 180.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-307-

CL

21A-457-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 208 / Label seq-ID: 1 - 207

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tetracycline repressor protein class D


Mass: 23245.309 Da / Num. of mol.: 2 / Mutation: A2S, N82A
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

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Non-polymers , 6 types, 276 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE


Mass: 444.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 45.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: precipitant: 0.1 M HEPES pH 7.5, 1.75M (NH4)2SO4, 5% PEG 400, 0.2M NaCl, protein: 0.1mL protein, 0.3mL 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris, pH 8.0, Protein/precipitant 2/2

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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: Aug 5, 2011
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32.94 Å / Num. obs: 40487 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.043 / Rrim(I) all: 0.149 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5722 / Rpim(I) all: 0.467 / Rrim(I) all: 1.052 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystalCleardata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FKK

5fkk


Resolution: 1.8→31.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.527 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24309 2039 5.1 %RANDOM
Rwork0.20905 ---
obs0.21075 38282 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.8→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 66 262 3520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133312
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173114
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.6434486
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5737185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63321.237194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9531530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
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_it1.7982.1171618
X-RAY DIFFRACTIONr_mcbond_other1.7982.1171617
X-RAY DIFFRACTIONr_mcangle_it3.0053.1662019
X-RAY DIFFRACTIONr_mcangle_other3.0043.1662020
X-RAY DIFFRACTIONr_scbond_it2.0132.371693
X-RAY DIFFRACTIONr_scbond_other2.0172.3731685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2883.4652468
X-RAY DIFFRACTIONr_long_range_B_refined5.52725.4643915
X-RAY DIFFRACTIONr_long_range_B_other5.50625.3893885
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6110 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 148 -
Rwork0.308 2688 -
obs--97.46 %
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)
11.59350.32642.21490.07070.43473.18180.0588-0.0253-0.00220.01630.00390.00920.0736-0.0613-0.06270.0584-0.0001-0.02120.08080.0140.046632.152711.657476.6763
20.3248-0.1717-0.12750.09610.03551.21980.0971-0.0575-0.0506-0.04880.04950.0264-0.1190.1482-0.14660.0797-0.03620.01510.1046-0.03170.043525.332815.70850.2717
32.17590.7907-0.92331.26870.06560.5563-0.0102-0.0173-0.21710.3273-0.1658-0.01320.1782-0.07860.1760.2092-0.05210.02420.0574-0.01120.03181.2063.988853.9531
40.59110.0515-0.88490.15020.1031.6712-0.0143-0.1142-0.021-0.0483-0.03180.0253-0.02460.05170.04610.0420.0066-0.00260.1365-0.01110.02731.925423.5275.786
50.3546-0.059-0.06090.30710.25460.58530.0201-0.0122-0.0202-0.0440.02430.0275-0.0547-0.0101-0.04430.0963-0.0203-0.01280.059-0.00790.03077.439218.870249.7929
610.647-5.1503-0.00242.53480.2391.3291-0.1393-0.4158-0.14690.00180.23130.0641-0.37150.19-0.0920.1136-0.05630.03450.0618-0.04490.113331.780332.167152.1484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 63
2X-RAY DIFFRACTION2A64 - 156
3X-RAY DIFFRACTION2A182 - 208
4X-RAY DIFFRACTION3A165 - 181
5X-RAY DIFFRACTION4B2 - 63
6X-RAY DIFFRACTION5B64 - 156
7X-RAY DIFFRACTION5B182 - 208
8X-RAY DIFFRACTION5B301 - 302
9X-RAY DIFFRACTION6B165 - 181

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