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- PDB-6fpm: TetR(D) T103A mutant in complex with tetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 6fpm
TitleTetR(D) T103A mutant in complex with tetracycline 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
TETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionFeb 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)23,8697
Polymers23,2581
Non-polymers6116
Water1,22568
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,73814
Polymers46,5172
Non-polymers1,22112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area7690 Å2
ΔGint-117 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.710, 68.710, 180.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

#1: Protein Tetracycline repressor protein class D


Mass: 23258.307 Da / Num. of mol.: 1 / Mutation: A2S, T103A
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 (E. coli) / Strain (production host): K-12 / References: UniProt: P0ACT4
#2: Chemical ChemComp-TAC / TETRACYCLINE


Mass: 444.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O8 / 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.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 24% PEG 400, 70mM MgCl2. 2mM TC, 14.55mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→64.22 Å / Num. obs: 19026 / % possible obs: 99.6 % / Redundancy: 14.1 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.059 / Net I/σ(I): 24.89
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 13.44 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1353 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FPL

6fpl


Resolution: 1.85→64.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.901 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26727 979 5.1 %RANDOM
Rwork0.21909 ---
obs0.22146 18047 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å2-0 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.85→64.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 37 68 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191731
X-RAY DIFFRACTIONr_bond_other_d0.0010.021647
X-RAY DIFFRACTIONr_angle_refined_deg1.8772.0152375
X-RAY DIFFRACTIONr_angle_other_deg0.87833764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1523.37383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50815295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3841517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02419
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_it2.8252.498824
X-RAY DIFFRACTIONr_mcbond_other2.8242.499823
X-RAY DIFFRACTIONr_mcangle_it4.2373.7251043
X-RAY DIFFRACTIONr_mcangle_other4.2353.7241044
X-RAY DIFFRACTIONr_scbond_it2.882.827906
X-RAY DIFFRACTIONr_scbond_other2.8782.827907
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4434.1231333
X-RAY DIFFRACTIONr_long_range_B_refined6.81420.0732076
X-RAY DIFFRACTIONr_long_range_B_other6.81520.0272060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.846→1.894 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 72 -
Rwork0.333 1276 -
obs--97.4 %
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)
10.9431-0.44971.43620.6113-0.01463.37660.03330.00960.06690.02780.0259-0.11450.1759-0.0503-0.05920.1125-0.06-0.01320.2958-0.01650.135219.035828.445215.0527
21.11360.70340.69080.52030.17071.56810.21090.20940.10120.23380.11730.14490.04350.0071-0.32810.31180.16290.02690.19930.01740.126725.276333.079640.4764
39.32192.27865.09750.7341.24773.25310.2483-0.03510.49170.1183-0.17490.14670.31440.027-0.07330.1840.0117-0.06680.1856-0.03950.300150.563120.611737.3743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 66
2X-RAY DIFFRACTION1A1211 - 1214
3X-RAY DIFFRACTION2A67 - 155
4X-RAY DIFFRACTION2A180 - 208
5X-RAY DIFFRACTION2A1209 - 1210
6X-RAY DIFFRACTION3A167 - 179

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