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- PDB-6rbm: TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM -

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Basic information

Entry
Database: PDB / ID: 6rbm
TitleTETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE 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-MIY / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 11, 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9259
Polymers23,2301
Non-polymers6948
Water1,09961
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,85018
Polymers46,4612
Non-polymers1,38916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area9000 Å2
ΔGint-176 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.670, 67.670, 178.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Tetracycline repressor protein class D


Mass: 23230.299 Da / Num. of mol.: 1 / Mutation: A2S, E147A
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
#2: Chemical ChemComp-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE


Mass: 457.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N3O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: precipitant: 0.5M (NH4)2SO4, 0.68M Li2SO4, 0.1M Na-citrate, protein: 0.1mL protein, 0.1mL 2mM minoTc, 0.0005mL 3M MgCl2, 100 mM NaCl, 50 mM Tris pH 8.0, ratio 2/2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.05→63.3 Å / Num. obs: 13397 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 43.5 Å2 / Rrim(I) all: 0.053 / Net I/σ(I): 22.74
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 7.15 % / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2117 / Rrim(I) all: 1.09 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FPL

6fpl


Resolution: 2.05→47.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.082 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.208 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26329 1028 7.7 %RANDOM
Rwork0.21134 ---
obs0.21553 12379 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.54 Å2
Refinement stepCycle: 1 / Resolution: 2.05→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 40 61 1720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171577
X-RAY DIFFRACTIONr_angle_refined_deg1.841.6722306
X-RAY DIFFRACTIONr_angle_other_deg1.3821.5923633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56721.38394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.551515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021924
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02363
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_it2.8723.663832
X-RAY DIFFRACTIONr_mcbond_other2.8723.663831
X-RAY DIFFRACTIONr_mcangle_it4.4145.4881040
X-RAY DIFFRACTIONr_mcangle_other4.4125.4871041
X-RAY DIFFRACTIONr_scbond_it2.873.85861
X-RAY DIFFRACTIONr_scbond_other2.8693.852862
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4535.7271267
X-RAY DIFFRACTIONr_long_range_B_refined6.91243.9551982
X-RAY DIFFRACTIONr_long_range_B_other6.91143.9081975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 96 -
Rwork0.369 867 -
obs--99.07 %
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)
13.161-0.55042.4320.1215-0.62674.0287-0.10.20180.05510.01510.0182-0.02840.2376-0.01430.08180.2313-0.0216-0.07520.2239-0.04530.094718.94328.289313.1569
20.70550.81860.2840.9530.37980.95480.08250.0760.12650.08750.10270.13170.1286-0.0302-0.18520.33820.2887-0.02950.27360.02170.098224.892832.13639.3404
311.75054.2821-2.67351.5626-0.98690.7341-0.28040.57670.4708-0.14380.24040.16220.31880.02620.03990.49990.30080.15550.23830.12660.169949.565720.564835.9248
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

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