6S62

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.

• PDB DOI: https://doi.org/10.2210/pdb6S62/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-02 Released: 2020-10-14 
• Deposition Author(s): Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.260 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form.

Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 329.72 kDa 
• Atom Count: 22,926 
• Modelled Residue Count: 2,906 
• Deposited Residue Count: 2,964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionate catabolic protein PrpD	A, B, C, D, E, F	494	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: prpD, PA0792 EC: 4.2.1.79
UniProt
Find proteins for Q9I5E6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5E6  Go to UniProtKB:  Q9I5E6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.260 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.48	α = 90
b = 124.54	β = 116.85
c = 126.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M019411/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/R005435/1

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description