5FDN | pdb_00005fdn

Crystal structure of phosphoenolpyruvate carboxylase from Arabidopsis thaliana in complex with aspartate and citrate

• PDB DOI: https://doi.org/10.2210/pdb5FDN/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-12-16 Released: 2017-02-08 
• Deposition Author(s): Connell, M.B., Lee, M.J.Y., Plaxton, W.C., Jia, Z.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal structure of phosphoenolpyruvate carboxylase from Arabidopsis thaliana in complex with aspartate and citrate

Connell, M.B., Lee, M.J.Y., Plaxton, W.C., Jia, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 225.32 kDa 
• Atom Count: 16,218 
• Modeled Residue Count: 1,814 
• Deposited Residue Count: 1,974 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxylase 3	A, B	987	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PPC3, PEPC, PPC, At3g14940, K15M2.8 EC: 4.1.1.31
UniProt
Find proteins for Q84VW9 (Arabidopsis thaliana) Explore Q84VW9  Go to UniProtKB:  Q84VW9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	D [auth A], F [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
ASP	C [auth A], E [auth B]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264.26	α = 90
b = 268.13	β = 90
c = 77.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Connell, M.B., Lee, M.J.Y., Plaxton, W.C., Jia, Z.

---

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN203705-2013

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Refinement description