4D5F | pdb_00004d5f

tetracycline repressor class H, apo form

• PDB DOI: https://doi.org/10.2210/pdb4D5F/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mannheimia haemolytica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-04 Released: 2016-01-20 
• Deposition Author(s): Palm, G.J., Quast, J., Hinrichs, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Domain Movement in Tetracycline Repressor Classes

Palm, G.J., Quast, J., 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: 23.4 kDa 
• Atom Count: 1,684 
• Modeled Residue Count: 194 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETRACYCLINE RESISTANCE REPRESSOR PROTEIN	A	206	Mannheimia haemolytica	Mutation(s): 0
UniProt
Find proteins for Q9Z358 (Mannheimia haemolytica) Explore Q9Z358  Go to UniProtKB:  Q9Z358

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.456	α = 90
b = 109.037	β = 90
c = 69.687	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: 2016-01-20 
Deposition Author(s): Palm, G.J., Quast, J., Hinrichs, W.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description