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- PDB-2tct: THE COMPLEX FORMED BETWEEN TET REPRESSOR AND TETRACYCLINE-MG2+ RE... -

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Basic information

Entry
Database: PDB / ID: 2tct
TitleTHE COMPLEX FORMED BETWEEN TET REPRESSOR AND TETRACYCLINE-MG2+ REVEALS MECHANISM OF ANTIBIOTIC RESISTANCE
ComponentsTETRACYCLINE REPRESSOR
KeywordsTRANSCRIPTION 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-CHLOROTETRACYCLINE / Tetracycline repressor protein class D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsHinrichs, W. / Kisker, C. / Saenger, W.
Citation
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.
#1: Journal: Science / Year: 1994
Title: Structure of the Tet Repressor-Tetracycline Complex and Regulation of Antibiotic Resistance
Authors: Hinrichs, W. / Kisker, C. / Duevel, M. / Mueller, A. / Tovar, K. / Hillen, W. / Saenger, W.
History
DepositionMar 2, 1995Processing site: BNL
SupersessionApr 3, 1996ID: 1TCT
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 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.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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7763
Polymers23,2721
Non-polymers5032
Water2,432135
1
A: TETRACYCLINE REPRESSOR
hetero molecules

A: TETRACYCLINE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5516
Polymers46,5452
Non-polymers1,0064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area7540 Å2
ΔGint-72 kcal/mol
Surface area18080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.780, 68.780, 181.450
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-347-

HOH

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Components

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


Mass: 23272.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: REMAULT E.,STANSSENS P.,FIERS W. PLASMID VECTORS FOR HIGH-EFFICIENCY EXPRESSION CONTROLLED BY THE PL PROMOTER OF COLIPHAGE LAMBDA. GENE 15, 81-93 (1981).
Plasmid: PWH904 (K. TOVAR, PH.D. THESIS, UNIV. ERLANGEN-NUERNBERG, 1989)
Production host: Escherichia coli (E. coli) / Strain (production host): K12 DELTA H1 DELTA TRP / References: UniProt: P0ACT4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CTC / 7-CHLOROTETRACYCLINE


Mass: 478.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal
*PLUS
Density % sol: 42 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein1drop
21 mMTc1drop
310 mM1dropMgCl2
435 %satammonium sulfate1drop
550 mMTris-HCl1drop
635 %satammonium sulfate1reservoir
75 mMammonium sulfate1reservoir
850 mMTris-HCl1reservoir

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Data collection

ReflectionResolution: 2→20 Å / Num. obs: 14105 / % possible obs: 92.6 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.18 --
obs0.18 12229 93.8 %
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 34 135 1742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection all: 12229 / Num. reflection obs: 10754 / Rfactor all: 0.183 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg20.1
X-RAY DIFFRACTIONx_improper_angle_deg1.55

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