5FDN

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
R-Value Work: 0.173
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q84VW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ASP Query on ASP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.193
R-Value Work: 0.173
R-Value Observed: 0.173
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

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Entry History & Funding Information

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

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

Revision History (Full details and data files)

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

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5FDN

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)