1QPI | pdb_00001qpi

CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1QPI/pdb
• NAKB: 1QPI

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-05-25 Released: 2000-02-28 
• Deposition Author(s): Orth, P., Schnappinger, D., Hillen, W., Saenger, W., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.307 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system.

Orth, P., Schnappinger, D., Hillen, W., Saenger, W., Hinrichs, W.

(2000) Nat Struct Biol 7: 215-219

• PubMed: 10700280 
• DOI: https://doi.org/10.1038/73324
• Primary Citation Related Structures: 
  1QPI


• PubMed Abstract: 
  

  The tetracycline repressor (TetR) regulates the most abundant resistance mechanism against the antibiotic tetracycline in grain-negative bacteria. The TetR protein and its mutants are commonly used as control elements to regulate gene expression in higher eukaryotes. We present the crystal structure of the TetR homodimer in complex with its palindromic DNA operator at 2.5 A resolution. Comparison to the structure of TetR in complex with the inducer tetracycline-Mg2+ allows the mechanism of induction to be deduced. Inducer binding in the repressor core initiates conformational changes starting with C-terminal unwinding and shifting of the short helix a6 in each monomer. This forces a pendulum-like motion of helix a4, which increases the separation of the attached DNA binding domains by 3 A, abolishing the affinity of TetR for its operator DNA.

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Organizational Affiliation: 
• Institut für Chemie, Kristallographie, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.08 kDa 
• Atom Count: 2,203 
• Modeled Residue Count: 225 
• Deposited Residue Count: 233 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TETRACYCLINE REPRESSOR)	C [auth A]	203	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACT4 (Escherichia coli) Explore P0ACT4  Go to UniProtKB:  P0ACT4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3')	A [auth M]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')	B [auth N]	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.307 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.04	α = 90
b = 193.2	β = 90
c = 91.75	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-28 
Deposition Author(s): Orth, P., Schnappinger, D., Hillen, W., Saenger, W., Hinrichs, W.

Revision History  

• Version 1.0: 2000-02-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations