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- PDB-5fkl: TetR(D) H100A mutant in complex with anhydrotetracycline and magnesium -

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Basic information

Entry
Database: PDB / ID: 5fkl
TitleTetR(D) H100A 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
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: 1.9 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 / Derived calculations ...Data collection / Derived calculations / 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 / pdbx_struct_special_symmetry
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_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 / _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

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Assembly

Deposited unit
A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8747
Polymers23,2211
Non-polymers6536
Water1,15364
1
A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR, CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,74914
Polymers46,4432
Non-polymers1,30612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6780 Å2
ΔGint-94.8 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.557, 66.557, 179.681
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-301-

SO4

21A-2010-

HOH

31A-2050-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TETRACYCLINE REPRESSOR, CLASS D


Mass: 23221.264 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

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Non-polymers , 5 types, 70 molecules

#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-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE
Crystal growTemperature: 295 K
Details: 0.4 M (NH4)2SO4, 0.7 M LI2SO4, 0.1 M SODIUM CITRATE, 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: 1.9→62 Å / Num. obs: 15800 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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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: 1.9→62.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.051 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26545 808 5.1 %RANDOM
Rwork0.21474 ---
obs0.21695 15187 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.078 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2--2.78 Å20 Å2
3----5.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 40 64 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191684
X-RAY DIFFRACTIONr_bond_other_d0.0010.021621
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9982289
X-RAY DIFFRACTIONr_angle_other_deg0.71433702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8085203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42223.49483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0521517
X-RAY DIFFRACTIONr_chiral_restr0.0610.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
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_it1.6643.42812
X-RAY DIFFRACTIONr_mcbond_other1.6653.42811
X-RAY DIFFRACTIONr_mcangle_it2.655.1071012
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.873.693872
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: 1.905→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 52 -
Rwork0.326 1072 -
obs--94.14 %
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)
11.5427-0.08312.16640.0493-0.06853.12990.07230.24710.09130.0335-0.12880.00210.18730.24090.05640.058-0.0702-0.04050.2777-0.01120.132718.949728.009813.2113
21.1988-0.25710.37570.09770.14651.40660.05690.09670.00190.0417-0.02850.01540.30910.0068-0.02830.1061-0.0373-0.00020.0444-0.01510.175622.344827.223635.3722
31.1636-0.1942-0.30990.03660.00010.99290.06070.091-0.1088-0.0122-0.01820.0359-0.059-0.0429-0.04250.07250.02010.00720.0414-0.02310.226524.729633.057435.4954
40.49690.2780.020.37020.01120.1840.0171-0.0558-0.09430.1041-0.05860.06310.13120.04540.04150.18310.02080.01090.02220.00640.19238.370527.854144.0855
56.0999-4.0978-1.69164.888-2.50026.6685-0.05470.02930.12720.1409-0.0091-0.1625-0.167-0.03010.06380.0985-0.0139-0.01970.03090.00830.163919.791634.696635.0919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 106
3X-RAY DIFFRACTION3A107 - 159
4X-RAY DIFFRACTION4A164 - 208
5X-RAY DIFFRACTION5A222 - 223

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