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- PDB-2xb5: Tet repressor (class D) in complex with 7-Iodotetracycline -

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Basic information

Entry
Database: PDB / ID: 2xb5
TitleTet repressor (class D) in complex with 7-Iodotetracycline
ComponentsTETRACYCLINE REPRESSOR PROTEIN CLASS D
KeywordsTRANSCRIPTION / ANTIBIOTIC RESISTANCE / METAL-BINDING / TRANSCRIPTION REGULATION
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
7-IODOTETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsKisker, C. / Saenger, W. / Hinrichs, W.
Citation
Journal: Science / Year: 1994
Title: Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance.
Authors: Hinrichs, W. / Kisker, C. / Duvel, M. / Muller, A. / Tovar, K. / Hillen, W. / Saenger, W.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Complex Formed between Tet Repressor and Tetracycline-Mg2+ Reveals Mechanism of Antibiotic Resistance.
Authors: Kisker, C. / Hinrichs, W. / Tovar, K. / Hillen, W. / Saenger, W.
History
DepositionApr 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._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_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.7May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8724
Polymers23,2721
Non-polymers6003
Water72140
1
A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN CLASS D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7458
Polymers46,5452
Non-polymers1,2006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6210 Å2
ΔGint-71.4 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 68.860, 180.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN CLASS D / TET REPRESSOR CLASS D


Mass: 23272.334 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-208
Source method: isolated from a genetically manipulated source
Details: 7-IODOTETRACYCLINE, MG-COMPLEX / Source: (gene. exp.) Escherichia coli / Plasmid: PWH904 / Production host: Escherichia coli K-12 / Variant (production host): DELTA H1 DELTA TRP / References: UniProt: P0ACT4
#2: Chemical ChemComp-I7T / 7-IODOTETRACYCLINE


Mass: 540.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21IN2O7
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.31 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: 10MICROL PROTEIN (0.2MM TETR, 1MM IODOTC, 5MM MGCL2), 5MICROL RESERVOIR (35% AMMONIUM SULPHATE, TRIS-HCL PH 7.2) VAPOUR DIFFUSSION HANGING DROP

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1993 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.45→64.55 Å / Num. obs: 7120 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 41.55 Å2 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→64.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.906 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 1.059 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23018 777 9.8 %RANDOM
Rwork0.16163 ---
obs0.16847 7120 99.65 %-
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: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 33 40 1713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211703
X-RAY DIFFRACTIONr_bond_other_d0.0020.021143
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9932317
X-RAY DIFFRACTIONr_angle_other_deg1.03732773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2923.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.35415289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8721516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
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_it0.721.51030
X-RAY DIFFRACTIONr_mcbond_other0.1271.5418
X-RAY DIFFRACTIONr_mcangle_it1.39821646
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.223673
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7044.5671
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 55 -
Rwork0.225 515 -
obs--99.48 %
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)
14.6302-0.87666.95291.09-0.035312.22050.1470.30480.0085-0.033-0.0981-0.05740.20550.3847-0.04890.0333-0.0045-0.02430.1216-0.02430.092818.998728.7813.654
21.575-0.5348-0.39131.2632-0.28397.34780.0620.0766-0.1986-0.0129-0.07220.16490.5272-0.05180.01020.0564-0.0004-0.02280.0853-0.0190.107723.096428.694235.7755
34.2122-0.22580.54670.9446-0.81121.5430.12070.1839-0.2588-0.0805-0.13140.11310.0543-0.04480.01080.1180.02650.00270.064-0.03750.086232.823931.487239.5294
421.670612.8966-15.635543.0192-6.899719.8341-0.50450.0311-0.03180.3527-0.1048-0.45070.0064-0.90410.60930.05860.0438-0.03310.14430.00930.148921.213136.555735.1159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 45
2X-RAY DIFFRACTION1A46 - 64
3X-RAY DIFFRACTION2A65 - 93
4X-RAY DIFFRACTION2A94 - 100
5X-RAY DIFFRACTION2A101 - 106
6X-RAY DIFFRACTION3A156 - 165
7X-RAY DIFFRACTION3A166 - 181
8X-RAY DIFFRACTION3A107 - 123
9X-RAY DIFFRACTION3A124 - 155
10X-RAY DIFFRACTION3A182 - 208
11X-RAY DIFFRACTION4A222

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