4ABZ | pdb_00004abz

TetR(D) in Complex with Tigecycline and Magnesium, co-crystallized

• PDB DOI: https://doi.org/10.2210/pdb4ABZ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2011-12-12 Released: 2012-12-26 
• Deposition Author(s): Volkers, G., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.258 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.221 (DCC) 

Starting Model: experimental

Literature

TetR(D) in Complex with Tigecycline and Magnesium

Volkers, G., Hinrichs, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.01 kDa 
• Atom Count: 1,652 
• Modeled Residue Count: 195 
• 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 [auth AAA]	207	Escherichia coli	Mutation(s): 1  Gene Names: tetR
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
T1C (Subject of Investigation/LOI)	B [auth AAA]	TIGECYCLINE C29 H41 N5 O8 FPZLLRFZJZRHSY-HJYUBDRYSA-P
CL	D [auth AAA], E [auth AAA], F [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)	C [auth AAA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.221 (DCC) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.49	α = 90
b = 68.49	β = 90
c = 179.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Volkers, G., Hinrichs, W.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 2.0: 2020-04-29
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: 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
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description