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- PDB-5fko: TetR(D) E147A mutant in complex with anhydrotetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 5fko
TitleTetR(D) E147A mutant in complex with anhydrotetracycline and magnesium
ComponentsTETRACYCLINE REPRESSOR, CLASS D, E147A MUTANT
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
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: 1.85 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_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_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_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_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, E147A MUTANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8588
Polymers23,2301
Non-polymers6287
Water1,928107
1
A: TETRACYCLINE REPRESSOR, CLASS D, E147A MUTANT
hetero molecules

A: TETRACYCLINE REPRESSOR, CLASS D, E147A MUTANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,71716
Polymers46,4612
Non-polymers1,25614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6550 Å2
ΔGint-145.8 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.467, 68.467, 178.787
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-2015-

HOH

21A-2090-

HOH

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Components

#1: Protein TETRACYCLINE REPRESSOR, CLASS D, E147A MUTANT


Mass: 23230.299 Da / Num. of mol.: 1 / 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
#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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.25 Å3/Da / Density % sol: 45.45 % / Description: NONE
Crystal growTemperature: 295 K / pH: 6.5
Details: 15% PEG 4000, 100 MM MES PH 6.5, 600 MM 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: MARRESEARCH SX-165 / 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: 1.85→64.6 Å / Num. obs: 18638 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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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: 1.85→64.02 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.802 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25993 953 5.1 %RANDOM
Rwork0.21055 ---
obs0.21293 17674 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å20 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.85→64.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 37 107 1714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191630
X-RAY DIFFRACTIONr_bond_other_d0.0010.021575
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9922214
X-RAY DIFFRACTIONr_angle_other_deg0.72933593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.035196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72923.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0531515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
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_it1.3742.773790
X-RAY DIFFRACTIONr_mcbond_other1.3742.773789
X-RAY DIFFRACTIONr_mcangle_it2.1494.148984
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6132.989840
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: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 70 -
Rwork0.297 1281 -
obs--99.63 %
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)
11.4359-0.5432.02650.2725-0.60673.39040.02120.06320.08570.04580.0107-0.0870.19940.0104-0.03180.0639-0.0289-0.02910.2069-0.03680.127118.981528.620413.9241
20.21230.34190.39250.59180.53471.77340.04070.06540.02350.12710.11690.06450.1938-0.0095-0.15760.17270.0773-0.01790.1581-0.01370.129222.937328.672935.5643
32.1072-0.28940.02520.40350.76161.6164-0.02570.1710.0186-0.0088-0.02640.0359-0.03980.00770.05210.13130.10170.0330.1436-0.01140.161623.875135.499337.3038
41.15980.1075-0.26820.69330.04970.07760.22050.0821-0.09220.081-0.2205-0.0106-0.0167-0.03200.28320.0954-0.01480.1223-0.00260.091938.594528.75944.6528
50.3835-1.02911.00625.5009-0.8734.16570.0295-0.0103-0.06130.09030.14770.0801-0.0099-0.1388-0.17730.1580.0894-0.01490.149-0.03140.134220.748936.164435.2711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 106
3X-RAY DIFFRACTION3A107 - 155
4X-RAY DIFFRACTION4A165 - 208
5X-RAY DIFFRACTION5A1209 - 1210

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