8OVN | pdb_00008ovn

X-ray structure of the SF-iGluSnFR-S72A

PDB DOI: https://doi.org/10.2210/pdb8OVN/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: 2.60 Å
R-Value Free:
0.253 (Depositor), 0.251 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8OVN

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

Literature

X-ray structure of the SF-iGluSnFR-S72A

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

To be published.

Macromolecule Content

Total Structure Weight: 58.21 kDa
Atom Count: 4,019
Modeled Residue Count: 504
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative periplasmic binding transport protein,Green fluorescent protein	A	518	Shigella flexneri	Mutation(s): 22 Gene Names: ybeJ, SF0626, GFP
UniProt
Find proteins for P37902 (Escherichia coli (strain K12)) Explore P37902 Go to UniProtKB: P37902
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P42212 P37902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-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
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.253 (Depositor), 0.251 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.14	α = 90
b = 106.14	β = 90
c = 108.14	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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: 2024-10-23
Changes: Data collection, Structure summary

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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.