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- PDB-2o7o: Crystal structure analysis of TetR(D) complex with doxycycline -

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Basic information

Entry
Database: PDB / ID: 2o7o
TitleCrystal structure analysis of TetR(D) complex with doxycycline
ComponentsTetracycline repressor protein class D
KeywordsTRANSCRIPTION REGULATOR / helix-turn-helix / metal coordination
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 / DNA-binding HTH domain, TetR-type ...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
Chem-DXT / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAleksandrov, A. / Proft, J. / Hinrichs, W.
CitationJournal: Chembiochem / Year: 2007
Title: Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments
Authors: Aleksandrov, A. / Proft, J. / Hinrichs, W. / Simonson, T.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9246
Polymers23,2881
Non-polymers6365
Water1,838102
1
A: Tetracycline repressor protein class D
hetero molecules

A: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84812
Polymers46,5772
Non-polymers1,27110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area8520 Å2
ΔGint-80 kcal/mol
Surface area18770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.830, 65.830, 179.502
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

DetailsThe second part of the biological homodimer is generated by the two fold axis: -x+1, -y+1,z.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tetracycline repressor protein class D


Mass: 23288.334 Da / Num. of mol.: 1 / Fragment: residues 2-208 / Mutation: A2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pwh 610 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 DELTA H1 DELTA TRP / References: UniProt: P0ACT4

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Non-polymers , 5 types, 107 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE


Mass: 444.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O8 / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.1M AMMONIUM SULPHATE, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8011 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8011 Å / Relative weight: 1
ReflectionResolution: 1.89→19.34 Å / Num. all: 16248 / Num. obs: 16248 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 29.6
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 785 / Rsym value: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCD 165data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TCT

2tct


Resolution: 1.89→19.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.395 / SU ML: 0.129 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24323 817 5 %RANDOM
Rwork0.2021 ---
all0.20419 16248 --
obs0.20419 15374 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.971 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2--1.64 Å20 Å2
3----3.29 Å2
Refine analyzeLuzzati coordinate error free: 0.161 Å
Refinement stepCycle: LAST / Resolution: 1.89→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 40 102 1783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211731
X-RAY DIFFRACTIONr_bond_other_d0.0020.021168
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9962357
X-RAY DIFFRACTIONr_angle_other_deg1.13932832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10323.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52115297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1061517
X-RAY DIFFRACTIONr_chiral_restr0.170.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONr_nbd_refined0.2440.2481
X-RAY DIFFRACTIONr_nbd_other0.2070.21285
X-RAY DIFFRACTIONr_nbtor_refined0.1970.2914
X-RAY DIFFRACTIONr_nbtor_other0.1020.2937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.297
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.221
X-RAY DIFFRACTIONr_mcbond_it1.6151.51323
X-RAY DIFFRACTIONr_mcbond_other0.3431.5422
X-RAY DIFFRACTIONr_mcangle_it1.90221669
X-RAY DIFFRACTIONr_scbond_it3.0973772
X-RAY DIFFRACTIONr_scangle_it4.2334.5688
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 77 -
Rwork0.256 1099 -
obs--99.41 %

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