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- PDB-5fkk: TetR(D) N82A mutant in complex with anhydrotetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 5fkk
TitleTetR(D) N82A mutant in complex with anhydrotetracycline and magnesium
ComponentsTETRACYCLINE REPRESSOR, CLASS D
KeywordsTRANSCRIPTION / REPRESSOR / ANTIBIOTIC RESISTANCE / TETR
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
TRIETHYLENE GLYCOL / 5A,6-ANHYDROTETRACYCLINE / Repressor protein / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWerten, S. / Schneider, J. / Palm, G.J. / Hinrichs, W.
CitationJournal: 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
DepositionOct 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 10, 2024Group: 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 / struct_site
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_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.ptnr1_label_seq_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.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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, CLASS D
B: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,70116
Polymers46,4912
Non-polymers1,21014
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-107.7 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.231, 68.231, 179.247
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-306-

CL

21A-2090-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TETRACYCLINE REPRESSOR, CLASS D


Mass: 23245.309 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: C6G9U5, UniProt: P0ACT4*PLUS

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Non-polymers , 7 types, 250 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TDC / 5A,6-ANHYDROTETRACYCLINE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.24 Å3/Da / Density % sol: 45.18 % / Description: NONE
Crystal growTemperature: 295 K / pH: 7.5
Details: 1.5 M (NH4)2SO4, 0.1 M HEPES PH 7.5, 5% PEG 400, 0.2 M NACL, 1 MM 5A,6-ANHYDROTETRACYCLINE, 7.5 MM MGCL2 AT 295 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8031
DetectorType: RAYONIX SX-165mm / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 1.75→63.3 Å / Num. obs: 43782 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.9
Reflection shellResolution: 1.75→1.77 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D7M

4d7m


Resolution: 1.75→63.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.179 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25424 2183 5 %RANDOM
Rwork0.20652 ---
obs0.20892 41206 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.433 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.75→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 69 236 3467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193292
X-RAY DIFFRACTIONr_bond_other_d0.0010.023188
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9854455
X-RAY DIFFRACTIONr_angle_other_deg0.74737289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1445399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85223.457162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
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_it1.4222.3241596
X-RAY DIFFRACTIONr_mcbond_other1.4232.3241595
X-RAY DIFFRACTIONr_mcangle_it2.3153.4731989
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7242.6171696
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.746→1.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 145 -
Rwork0.258 3008 -
obs--99.46 %
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)
11.4860.33922.07580.16940.26213.39360.1045-0.0133-0.0560.04640.02370.00340.097-0.059-0.12820.03820.0038-0.04630.09630.02440.127432.043311.61576.0067
20.406-0.06230.19020.0240.10252.71130.0876-0.0623-0.0619-0.02210.0484-0.0188-0.0190.1623-0.1360.053-0.0436-0.00630.1313-0.02990.14727.827311.784554.439
30.3286-0.2636-0.60370.21240.48471.19660.1246-0.2080.1033-0.10130.1759-0.0866-0.22850.3193-0.30050.0776-0.1070.06370.2225-0.00830.194425.725818.402152.8154
40.61610.019-0.40350.35350.34320.63770.0669-0.0505-0.1403-0.0254-0.0569-0.0765-0.0474-0.0143-0.010.1087-0.0286-0.02610.06690.01130.128511.427911.293745.8068
51.6315-5.2191-3.146116.793210.07846.0704-0.01230.0074-0.05930.0372-0.10290.24670.0164-0.02250.11520.0423-0.0549-0.00280.17170.01350.11830.758816.22954.8118
61.24910.1129-1.66530.10540.07012.7917-0.0457-0.1757-0.04-0.0725-0.02680.0176-0.08140.1240.07250.05220.0034-0.00880.1651-0.02950.13631.972823.368175.209
70.53420.03720.06310.06940.29131.78870.0326-0.07560.0199-0.06820.02650.0181-0.18790.0421-0.05910.1228-0.0464-0.01620.0607-0.01130.13365.4122.983953.4727
81.1150.59750.21660.83880.78480.9063-0.0227-0.0582-0.0161-0.02870.0060.0114-0.01340.02670.01670.0856-0.056-0.03960.0668-0.00790.14196.103215.764251.6669
90.8047-0.23330.16990.08440.02260.38650.2220.05980.0538-0.1365-0.0122-0.0515-0.2470.0507-0.20990.3606-0.04090.15910.0282-0.00340.166819.920222.657443.5635
104.8316-3.37025.62697.1763-3.39176.6135-0.0637-0.11940.0587-0.3010.0054-0.0676-0.0967-0.15030.05830.1328-0.0259-0.02510.0244-0.01280.04533.441715.577653.9624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 106
3X-RAY DIFFRACTION3A107 - 157
4X-RAY DIFFRACTION4A162 - 208
5X-RAY DIFFRACTION5A222 - 223
6X-RAY DIFFRACTION6B2 - 64
7X-RAY DIFFRACTION7B65 - 106
8X-RAY DIFFRACTION8B107 - 154
9X-RAY DIFFRACTION9B166 - 208
10X-RAY DIFFRACTION10B222 - 223

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