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- PDB-4abz: TetR(D) in Complex with Tigecycline and Magnesium, co-crystallized -

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Entry
Database: PDB / ID: 4abz
TitleTetR(D) in Complex with Tigecycline and Magnesium, co-crystallized
ComponentsTetracycline repressor protein class D
KeywordsTRANSCRIPTION
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. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
TIGECYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.886 Å
AuthorsVolkers, G. / Hinrichs, W.
CitationJournal: To be Published
Title: TetR(D) in Complex with Tigecycline and Magnesium
Authors: Volkers, G. / Hinrichs, W.
History
DepositionDec 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 2.0Apr 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / audit_author / audit_conform / chem_comp / citation / citation_author / database_PDB_matrix / diffrn / diffrn_source / entity / entity_poly / entity_src_gen / exptl_crystal_grow / pdbx_database_related / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _audit_author.identifier_ORCID / _chem_comp.formula ..._audit_author.identifier_ORCID / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.title / _diffrn.pdbx_serial_crystal_experiment / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_details / _entity_src_gen.host_org_details / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.SG_entry / _pdbx_database_status.pdb_format_compatible / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_atom_id_1 / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_standard_deviation / _pdbx_validate_rmsd_bond.bond_target_value / _pdbx_validate_rmsd_bond.bond_value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rrim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rrim_I_all / _struct.pdbx_CASP_flag / _struct.title / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Description: Model completeness
Details: improved refinement of the model, completing crystallization conditions etc.
Provider: author / Type: Coordinate replacement
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0076
Polymers23,2881
Non-polymers7185
Water75742
1
AAA: Tetracycline repressor protein class D
hetero molecules

AAA: Tetracycline repressor protein class D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01312
Polymers46,5772
Non-polymers1,43710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6350 Å2
ΔGint-104 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 68.490, 179.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Tetracycline repressor protein class D


Mass: 23288.334 Da / Num. of mol.: 1 / Mutation: A2S
Source method: isolated from a genetically manipulated source
Details: RA1 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Details (production host): pWH1950 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACT4
#2: Chemical ChemComp-T1C / TIGECYCLINE


Mass: 587.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N5O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein: 10.0 mg/mL TetR(D), 0.2M NaCl, 50 mM Tris/HCl, pH 8.0, 2mM [TigeTC], 2mM MgCl2. Precipitant: 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 8.0, 10mM MgCl2. Protein/precipitant 2+2 ...Details: Protein: 10.0 mg/mL TetR(D), 0.2M NaCl, 50 mM Tris/HCl, pH 8.0, 2mM [TigeTC], 2mM MgCl2. Precipitant: 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 8.0, 10mM MgCl2. Protein/precipitant 2+2 microL, against 0.5mL Precipitant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 18428 / % possible obs: 98.2 % / Redundancy: 14.15 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.05 / Net I/σ(I): 33.95
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 14.19 % / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1323 / Rrim(I) all: 1.9 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xpv

2xpv


Resolution: 1.886→48.477 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.7 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2583 880 5.067 %
Rwork0.2131 --
all0.215 --
obs-17367 98.219 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.603 Å2
Baniso -1Baniso -2Baniso -3
1-1.335 Å2-0 Å2-0 Å2
2--1.335 Å2-0 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 1.886→48.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 46 42 1638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171530
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.682229
X-RAY DIFFRACTIONr_angle_other_deg1.5391.6023522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0821.38394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24315279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5411515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_nbd_refined0.2370.2395
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21353
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2833
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.249
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.232
X-RAY DIFFRACTIONr_nbd_other0.2420.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_mcbond_it2.222.775788
X-RAY DIFFRACTIONr_mcbond_other2.2172.775787
X-RAY DIFFRACTIONr_mcangle_it3.274.135985
X-RAY DIFFRACTIONr_mcangle_other3.2694.136986
X-RAY DIFFRACTIONr_scbond_it2.5873.136853
X-RAY DIFFRACTIONr_scbond_other2.5853.137853
X-RAY DIFFRACTIONr_scangle_it4.034.5971244
X-RAY DIFFRACTIONr_scangle_other4.034.5971244
X-RAY DIFFRACTIONr_lrange_it5.63133.3641898
X-RAY DIFFRACTIONr_lrange_other5.63133.3411894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.886-1.9350.506740.4821046X-RAY DIFFRACTION88.4676
1.935-1.9880.347620.3051167X-RAY DIFFRACTION98.8737
1.988-2.0460.29550.2581159X-RAY DIFFRACTION100
2.046-2.1090.358650.2731113X-RAY DIFFRACTION99.2418
2.109-2.1780.27660.241066X-RAY DIFFRACTION100
2.178-2.2540.425570.2861019X-RAY DIFFRACTION95.8148
2.254-2.3390.29590.253968X-RAY DIFFRACTION95.8022
2.339-2.4350.301470.221991X-RAY DIFFRACTION100
2.435-2.5430.24440.215956X-RAY DIFFRACTION99.7009
2.543-2.6660.295510.222894X-RAY DIFFRACTION99.4737
2.666-2.810.263420.249870X-RAY DIFFRACTION99.8905
2.81-2.9810.287500.235810X-RAY DIFFRACTION99.768
2.981-3.1860.318430.215775X-RAY DIFFRACTION99.3925
3.186-3.440.205340.2728X-RAY DIFFRACTION99.3481
3.44-3.7680.226300.186668X-RAY DIFFRACTION98.5876
3.768-4.2110.239270.17608X-RAY DIFFRACTION98.2972
4.211-4.8590.161260.155554X-RAY DIFFRACTION99.6564
4.859-5.9420.254200.196470X-RAY DIFFRACTION99.5935
5.942-8.3670.168160.176389X-RAY DIFFRACTION100
8.367-48.4770.164120.188236X-RAY DIFFRACTION97.6378
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)
12.1598-0.71171.90010.2808-0.3723.16030.00810.13230.15090.0367-0.0207-0.07150.19520.08340.01260.02740.0052-0.01960.1214-0.02040.125918.961728.340313.366
20.80340.42220.60120.22480.28981.74920.11290.05780.06350.06930.01270.0524-0.0527-0.0352-0.12560.12830.07460.01360.0501-0.02040.132424.869433.264339.8096
37.65492.14740.57171.3032-0.41010.52350.00690.5084-0.0945-0.1146-0.0238-0.08630.14380.1620.01690.14810.0281-0.03220.091-0.0280.082849.201720.036436.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 63
2X-RAY DIFFRACTION1ALLAAA1212
3X-RAY DIFFRACTION2ALLAAA64 - 152
4X-RAY DIFFRACTION2ALLAAA182 - 208
5X-RAY DIFFRACTION2ALLAAA1209 - 1210
6X-RAY DIFFRACTION3ALLAAA166 - 181

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