5YR3 | pdb_00005yr3

Structure of sfYFP66BPA

PDB DOI: https://doi.org/10.2210/pdb5YR3/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2017-11-08 Released: 2019-01-30
Deposition Author(s): Kang, F., Wang, L., Wang, J.
Funding Organization(s): Ministry of Science and Technology (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.290 (Depositor), 0.291 (DCC)
R-Value Work:
0.244 (Depositor), 0.245 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5YR3

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

Literature

sfYFP66BPA

Kang, F., Wang, L.

To be published.

Macromolecule Content

Total Structure Weight: 25.43 kDa
Atom Count: 1,904
Modeled Residue Count: 225
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yellow fluorescent protein	A	225	Aequorea victoria	Mutation(s): 14 Gene Names: yfp
UniProt
Find proteins for A0A059PIR9 (Aequorea victoria) Explore A0A059PIR9 Go to UniProtKB: A0A059PIR9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A059PIR9
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: 1.90 Å
R-Value Free: 0.290 (Depositor), 0.291 (DCC)
R-Value Work: 0.244 (Depositor), 0.245 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.713	α = 90
b = 51.713	β = 90
c = 178.977	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2017YFA0503704

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2026-03-18
Changes: 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.