9LYL | pdb_00009lyl

The X-ray diffraction structure of photosensitizer protein PSP2

PDB DOI: https://doi.org/10.2210/pdb9LYL/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-20 Released: 2025-04-02
Deposition Author(s): Zhao, Y.M., Qi, C.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.232 (Depositor), 0.232 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The X-ray diffraction structure of photosensitizer protein PSP2

Zhao, Y.M., Qi, C.

To be published.

Macromolecule Content

Total Structure Weight: 25.43 kDa
Atom Count: 1,947
Modeled Residue Count: 225
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PSP2	A	225	Aequorea victoria	Mutation(s): 0
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BF6 Query on BF6	A	L-PEPTIDE LINKING	C₂₀ H₁₇ N₃ O₄		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.272 (Depositor), 0.272 (DCC)
R-Value Work: 0.232 (Depositor), 0.232 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.04	α = 90
b = 51.04	β = 90
c = 179.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0904101

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