4KQD

The crystal Structure of the N-terminal PAS domain of the F plasmid TraJ

• PDB DOI: https://doi.org/10.2210/pdb4KQD/pdb

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


• Deposited: 2013-05-14 Released: 2014-07-02 
• Deposition Author(s): Lu, J., Glover, J.N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.178 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

The crystal Structure of the N-terminal PAS domain of the F plasmid TraJ

Lu, J., Glover, J.N.M.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.03 kDa 
• Atom Count: 4,274 
• Modelled Residue Count: 454 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein TraJ	A, B, C, D	121	Escherichia coli K-12	Mutation(s): 0  Gene Names: ECOK12F072, traJ
UniProt
Find proteins for P06626 (Escherichia coli (strain K12)) Explore P06626  Go to UniProtKB:  P06626

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	E [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
DTD	F [auth B], H [auth D]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
GOL	G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.178 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.228	α = 90
b = 95.228	β = 90
c = 102.041	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Lu, J., Glover, J.N.M.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations