5KKU

Crystal structure of an N-terminal dehydratase from difficidin assembly line

• PDB DOI: https://doi.org/10.2210/pdb5KKU/pdb

• Classification: LYASE
• Organism(s): Bacillus amyloliquefaciens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-06-22 Released: 2016-12-21 
• Deposition Author(s): Keatinge-Clay, A.T., Zeng, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

A Dehydratase Provides Insights into Split Bimodules and Polypeptide Docking in trans-AT Polyketide Synthases

Zeng, J., Keatinge-Clay, A.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 138.67 kDa 
• Atom Count: 9,353 
• Modelled Residue Count: 1,148 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase type I	A, B, C, D	300	Bacillus amyloliquefaciens	Mutation(s): 0  Gene Names: difJ
UniProt
Find proteins for Q1RS44 (Bacillus amyloliquefaciens) Explore Q1RS44  Go to UniProtKB:  Q1RS44

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.355	α = 90.2
b = 73.981	β = 90.08
c = 94.178	γ = 90.66

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Keatinge-Clay, A.T., Zeng, J.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary