8TYU

High-resolution crystal structure of the SPX domain of XPR1 at 1.4 angstroms

PDB DOI: https://doi.org/10.2210/pdb8TYU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-25 Released: 2024-06-12
Deposition Author(s): Wang, H., Shears, S.B.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.191
R-Value Work: 0.162
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

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

Literature

Co-ordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate, IP8

wang, H., Shears, S.

To be published.

Macromolecule Content

Total Structure Weight: 41.98 kDa
Atom Count: 3,225
Modelled Residue Count: 348
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 53 member 1	A [auth B], B [auth A]	181	Homo sapiens	Mutation(s): 0 Gene Names: XPR1, SLC53A1, SYG1, X3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBH6 (Homo sapiens) Explore Q9UBH6 Go to UniProtKB: Q9UBH6
PHAROS: Q9UBH6 GTEx: ENSG00000143324
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBH6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.191
R-Value Work: 0.162
R-Value Observed: 0.162
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 47.798	β = 107.15
c = 71.682	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIAES080046

Revision History (Full details and data files)

Version 1.0: 2024-06-12
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 R01GM133198.