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- PDB-5fkm: TetR(D) T103A mutant in complex with anhydrotetracycline and magn... -

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Basic information

Entry
Database: PDB / ID: 5fkm
TitleTetR(D) T103A mutant in complex with anhydrotetracycline and magnesium, I4(1)22
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
5A,6-ANHYDROTETRACYCLINE / Repressor protein / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 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 1.4Jan 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8517
Polymers23,2581
Non-polymers5936
Water4,378243
1
A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,70214
Polymers46,5172
Non-polymers1,18512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6750 Å2
ΔGint-110.3 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.145, 68.145, 179.517
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-2047-

HOH

21A-2079-

HOH

31A-2112-

HOH

41A-2208-

HOH

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Components

#1: Protein TETRACYCLINE REPRESSOR, CLASS D


Mass: 23258.307 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.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 45.09 % / Description: NONE
Crystal growTemperature: 295 K / pH: 6.5
Details: 1.2 M (NH4)2SO4, 0.1 M MES PH 6.5, 110 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178
DetectorType: RIGAKU CCD / Detector: CCD / Details: OSMIC MULTIPLE LAYER OPTICS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.63→27.2 Å / Num. obs: 26692 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9
Reflection shellResolution: 1.63→1.73 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

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

4d7m


Resolution: 1.63→27.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.453 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21183 1335 5 %RANDOM
Rwork0.16982 ---
obs0.17187 25356 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.284 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.63→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 36 243 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191720
X-RAY DIFFRACTIONr_bond_other_d0.0010.021662
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9942345
X-RAY DIFFRACTIONr_angle_other_deg0.85133802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38123.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1511518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02414
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_it0.9211.215824
X-RAY DIFFRACTIONr_mcbond_other0.9211.215823
X-RAY DIFFRACTIONr_mcangle_it1.4621.8141030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3111.338896
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: 1.633→1.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 94 -
Rwork0.307 1794 -
obs--97.37 %
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)
10.7988-0.40241.2920.3448-0.45112.38180.00220.07940.03180.0318-0.0304-0.04490.05360.12870.02820.0128-0.0109-0.00580.0463-0.00980.039219.05928.154414.1103
20.32370.23920.12960.24670.20281.9564-0.01410.01020.00480.03140.02250.03750.07930.0049-0.00840.04620.0223-0.00770.0337-0.00550.052122.550728.415836.0734
31.7078-0.49880.10221.12361.09471.51750.10790.2011-0.0378-0.1240.0235-0.0255-0.12530.068-0.13140.06560.03940.00770.0592-0.00280.062925.978134.475835.8667
41.2855-0.143-0.18460.5148-0.01320.24090.0870.0805-0.1518-0.0434-0.11240.1050.0244-0.00340.02540.10480.0388-0.01020.054-0.01330.042737.716128.811545.5444
58.8240.677-4.86660.3006-1.57858.5250.10660.04240.28450.0660.0150.0149-0.3361-0.0626-0.12160.04490.0283-0.01540.0227-0.01340.019121.135436.151435.5496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 106
3X-RAY DIFFRACTION3A107 - 160
4X-RAY DIFFRACTION4A165 - 208
5X-RAY DIFFRACTION5A222 - 223

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