9B47 | pdb_00009b47

Y328F variant of P. indica phosphate transporter

PDB DOI: https://doi.org/10.2210/pdb9B47/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Serendipita indica
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2024-03-20 Released: 2025-03-26
Deposition Author(s): Gupta, M., Finer-Moore, J., Stroud, R.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.257 (Depositor), 0.250 (DCC)
R-Value Work:
0.225 (Depositor), 0.224 (DCC)
R-Value Observed:
0.233 (Depositor)

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

Roles of PiPT residues in phosphate binding and transport tested by mutagenesis

Gupta, M., Finer-Moore, J., Nelson, A., Kumar, H., Johri, A., Stroud, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 117.14 kDa
Atom Count: 6,661
Modelled Residue Count: 862
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate transporter	A, B	530	Serendipita indica	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for A8N031 (Serendipita indica) Explore A8N031 Go to UniProtKB: A8N031
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8N031
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.257 (Depositor), 0.250 (DCC)
R-Value Work: 0.225 (Depositor), 0.224 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.23	α = 90
b = 174.23	β = 90
c = 171.53	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Finer-Moore, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM24485

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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.