9LFB | pdb_00009lfb

Crystal structure of GpxB in complex with G3P

PDB DOI: https://doi.org/10.2210/pdb9LFB/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Marinobacter sp. DSM 11874
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-08 Released: 2025-11-26
Deposition Author(s): Wang, N., Li, C.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis and evolutionary pathways of glycerol-1-phosphate transport in marine bacteria.

Wang, N., Westermann, L.M., Li, M., Li, C., Murphy, A., Gu, Z., Silvano, E., Blindauer, C.A., Lidbury, I.D., Zhang, Y., Scanlan, D.J., Chen, Y.

(2025) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 35.45 kDa
Atom Count: 2,648
Modeled Residue Count: 295
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphonate ABC transporter, periplasmic phosphonate-binding protein	A	321	Marinobacter sp. DSM 11874	Mutation(s): 0 Gene Names: Maqu_3257
UniProt
Find proteins for A1U5Q9 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8)) Explore A1U5Q9 Go to UniProtKB: A1U5Q9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1U5Q9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G3P (Subject of Investigation/LOI) Query on G3P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.509	α = 90
b = 136.509	β = 90
c = 136.509	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-11-26
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.