5B61 | pdb_00005b61

Extra-superfolder GFP

PDB DOI: https://doi.org/10.2210/pdb5B61/pdb

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

Deposited: 2016-05-24 Released: 2017-06-14
Deposition Author(s): Park, H.H., Jang, T.-H., Choi, J.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The mechanism of folding robustness revealed by the crystal structure of extra-superfolder GFP.

Choi, J.Y., Jang, T.-H., Park, H.H.

(2017) FEBS Lett 591: 442-447

PubMed: 27990640 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12534
Primary Citation of Related Structures:
5B61

PubMed Abstract:
Stability of green fluorescent protein (GFP) is sometimes important for a proper practical application of this protein. Random mutagenesis and targeted mutagenesis have been used to create better-folded variants of GFP, including recently reported extra-superfolder GFP. Our aim was to determine the crystal structure of extra-superfolder GFP, which is more robustly folded and stable than GFP and superfolder GFP. The structural and structure-based mutagenesis analyses revealed that some of the mutations that created extra-superfolder GFP (F46L, E126K, N149K, and S208L) contribute to folding robustness by stabilizing extra-superfolder GFP with various noncovalent bonds.

Organizational Affiliation

School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, South Korea.

Macromolecule Content

Total Structure Weight: 160.86 kDa
Atom Count: 10,663
Modelled Residue Count: 1,349
Deposited Residue Count: 1,428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B, C, D, E A, B, C, D, E, F	238	Aequorea victoria	Mutation(s): 0 Gene Names: gfp
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 LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.12 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.301	α = 90
b = 98.763	β = 90
c = 263.804	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-06-14
Type: Initial release
Version 1.1: 2018-12-26
Changes: Data collection, Database references
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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.