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), 0.210 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.210 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (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

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Ligand Structure Quality Assessment

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.