9FBU | pdb_00009fbu

X-ray structure of the iGluSnFR3 in complex with L-glutamate

PDB DOI: https://doi.org/10.2210/pdb9FBU/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Shigella flexneri
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-05-14 Released: 2025-04-02
Deposition Author(s): Tarnawski, M., Hiblot, J., Leippe, P.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.211 (Depositor), 0.211 (DCC)
R-Value Work:
0.183 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray structure of the iGluSnFR3 in complex with L-glutamate

Tarnawski, M., Hiblot, J., Leippe, P.

To be published.

Macromolecule Content

Total Structure Weight: 58.18 kDa
Atom Count: 4,352
Modeled Residue Count: 502
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding transport protein,Green fluorescent protein	A	518	Shigella flexneri	Mutation(s): 36 Gene Names: ybeJ, SF0626, GFP
UniProt
Find proteins for A0A0H2UXX1 (Shigella flexneri) Explore A0A0H2UXX1 Go to UniProtKB: A0A0H2UXX1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UXX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU (Subject of Investigation/LOI) Query on GLU 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]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYS Query on GYS	A	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₅		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.211 (Depositor), 0.211 (DCC)
R-Value Work: 0.183 (Depositor), 0.182 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.76	α = 90
b = 100.84	β = 90
c = 73.29	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
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.