7LQO

Crystal structure of a genetically encoded red fluorescent peroxynitrite biosensor, pnRFP

PDB DOI: https://doi.org/10.2210/pdb7LQO/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Discosoma sp.
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2021-02-14 Released: 2022-03-16
Deposition Author(s): Huang, M., Ng, H.L., Pang, Y., Zhang, S., Fan, Y., Yeh, H., Xiong, Y., Li, X., Ai, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor

Pang, Y., Huang, M., Zhang, S., Fan, Y., Yeh, H., Xiong, Y., Li, X., Ng, H.L., Ai, H.

To be published.

Macromolecule Content

Total Structure Weight: 29.86 kDa
Atom Count: 1,933
Modelled Residue Count: 230
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
red fluorescent peroxynitrite biosensor pnRFP	A	262	Discosoma sp.	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
7N8 Query on 7N8	A	L-PEPTIDE LINKING	C₉ H₁₂ B N O₄		PHE
NRQ Query on NRQ	A	L-PEPTIDE LINKING	C₁₆ H₁₇ N₃ O₄ S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.203	α = 90
b = 34.567	β = 110.9
c = 88.815	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-03-16
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection, Derived calculations

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 R01GM133198.