8OVO | pdb_00008ovo

X-ray structure of the SF-iGluSnFR-S72A in complex with L-aspartate

PDB DOI: https://doi.org/10.2210/pdb8OVO/pdb

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

Deposited: 2023-04-26 Released: 2023-05-17
Deposition Author(s): Tarnawski, M., Hellweg, L., Bergner, A., Hiblot, J., Leippe, P., Johnsson, K.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 ?
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

X-ray structure of the SF-iGluSnFR-S72A in complex with L-aspartate

Tarnawski, M., Hellweg, L., Bergner, A., Hiblot, J., Leippe, P., Johnsson, K.

To be published.

Macromolecule Content

Total Structure Weight: 116.3 kDa
Atom Count: 8,788
Modelled Residue Count: 1,006
Deposited Residue Count: 1,036
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative periplasmic binding transport protein,Green fluorescent protein	A, B	518	Shigella flexneri	Mutation(s): 22 Gene Names: ybeJ, SF0626, GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for P37902 (Escherichia coli (strain K12)) Explore P37902 Go to UniProtKB: P37902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212P37902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP (Subject of Investigation/LOI) Query on ASP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A, B	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 ?
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 65.76	α = 90
b = 77.48	β = 90
c = 196.84	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

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-05-17
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Structure summary

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.