8R48

Structure of plastidial phosphorylase Pho1 from Solanum tuberosum at 2.2 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8R48/pdb

Classification: TRANSFERASE
Organism(s): Solanum tuberosum
Mutation(s): No

Deposited: 2023-11-13 Released: 2024-10-09
Deposition Author(s): Koulas, S.M., Leonidas, D.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.229
R-Value Work: 0.176
R-Value Observed: 0.178

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Kinetic and Structural Studies of the Plastidial Solanum tuberosum Phosphorylase

Koulas, S.M., Kyriakis, E., Tsagkarakou, A.S., Leonidas, D.D.

(2024) ACS Omega

DOI: https://doi.org/10.1021/acsomega.4c06313

Macromolecule Content

Total Structure Weight: 104.28 kDa
Atom Count: 7,004
Modelled Residue Count: 830
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic	A	916	Solanum tuberosum	Mutation(s): 0 EC: 2.4.1.1
UniProt
Find proteins for P04045 (Solanum tuberosum) Explore P04045 Go to UniProtKB: P04045
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04045
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.229
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.107	α = 90
b = 127.107	β = 90
c = 118.693	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	Greece	--

Revision History (Full details and data files)

Version 1.0: 2024-10-09
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.