6S87 | pdb_00006s87

Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in complex with oxaloacetate.

• PDB DOI: https://doi.org/10.2210/pdb6S87/pdb

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


• Deposited: 2019-07-08 Released: 2020-10-21 
• 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: 1.65 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in complex with oxaloacetate.

Wijaya, A.J., Brear, P., Dolan, S.K., Welch, 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 Evidence: equilibrium centrifugation

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: 167.65 kDa 
• Atom Count: 11,684 
• Modeled Residue Count: 1,431 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A, B, C, D	375	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: prpC, PA0795
UniProt
Find proteins for Q9I5E3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5E3  Go to UniProtKB:  Q9I5E3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAA (Subject of Investigation/LOI)	K [auth D]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M
GOL	E [auth A], F [auth B], G [auth B], H [auth C], I [auth D], J [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.64	α = 90
b = 86.76	β = 95.89
c = 161.84	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-21 
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: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description