4AUX | pdb_00004aux

Tet repressor class D in complex with 9-nitrotetracycline

• PDB DOI: https://doi.org/10.2210/pdb4AUX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2012-05-22 Released: 2012-05-30 
• Deposition Author(s): Orth, P., Saenger, W., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.258 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Tet Repressor Class D in Complex with 9-Nitrotetracycline and Magnesium

Orth, P., Saenger, W., Hinrichs, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.83 kDa 
• Atom Count: 1,731 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETRACYCLINE REPRESSOR PROTEIN CLASS D	A	207	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ACT4 (Escherichia coli) Explore P0ACT4  Go to UniProtKB:  P0ACT4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XTC	B [auth A]	(4S,4aS,5aR,12aS)-4-(dimethylamino)-3,10,12,12a-tetrahydroxy-9-nitro-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide C21 H21 N3 O9 IEJWCNPEOOQYLP-CROFIWJMSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.258 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.1	α = 90
b = 69.1	β = 90
c = 182.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Orth, P., Saenger, W., Hinrichs, W.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-05-22
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description