6T5M | pdb_00006t5m

Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate.

• PDB DOI: https://doi.org/10.2210/pdb6T5M/pdb

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


• Deposited: 2019-10-16 Released: 2020-09-30 
• Deposition Author(s): Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.227 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate.

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 129.14 kDa 
• Atom Count: 8,901 
• Modeled Residue Count: 1,105 
• Deposited Residue Count: 1,192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methylisocitrate lyase	A [auth C], B [auth A], C [auth D], D [auth B]	298	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: prpB, PA0796 EC: 4.1.3.30
UniProt
Find proteins for Q9I5E2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5E2  Go to UniProtKB:  Q9I5E2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYR (Subject of Investigation/LOI)	F [auth C], H [auth A], J [auth D], L [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth C], G [auth A], I [auth D], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.227 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.49	α = 90
b = 59.4	β = 120.3
c = 147.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Wijaya, A.J., Brear, P., Dolan, S.K., Welch, M.

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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: 2020-09-30
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-24
  Changes: Refinement description