8OJQ | pdb_00008ojq

Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 T778 mutant with bound phosphate

PDB DOI: https://doi.org/10.2210/pdb8OJQ/pdb

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-03-24 Released: 2024-04-03
Deposition Author(s): Haesaerts, S., Loris, R., Larsen, P.
Funding Organization(s): United States Department of Agriculture (USDA), Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants

Meyer, T.J., Sheng, J., Haesaerts, S., Frausto, K., O'Leary, S., Loris, R., Larsen, P.B.

To be published.

Macromolecule Content

Total Structure Weight: 223.01 kDa
Atom Count: 14,446
Modeled Residue Count: 1,796
Deposited Residue Count: 1,948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxylase 1	A, B	974	Arabidopsis thaliana	Mutation(s): 1 Gene Names: PPC1, p107, At1g53310, F12M16.21 EC: 4.1.1.31
UniProt
Find proteins for Q9MAH0 (Arabidopsis thaliana) Explore Q9MAH0 Go to UniProtKB: Q9MAH0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9MAH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128	α = 90
b = 159.84	β = 90
c = 141.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
United States Department of Agriculture (USDA)	United States	2021-67014-34888
Research Foundation - Flanders (FWO)	Belgium	G011420N

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.