3P28 | pdb_00003p28

Structure of a Circular Permutant of Green Fluorescent Protein

PDB DOI: https://doi.org/10.2210/pdb3P28/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-10-01 Released: 2011-10-05
Deposition Author(s): Melief, E.H., Kim, H., Kim, T.S., Wachter, R.M., Tonge, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.237 (Depositor), 0.179 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3P28

This is version 3.0 of the entry. See complete history.

Literature

Construction and Characterization of a Stable Circular Permutant of Green Fluorescent Protein

Melief, E.H., Kim, H., Kim, T.S., Wachter, R.M., Tonge, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 27.24 kDa
Atom Count: 2,186
Modeled Residue Count: 235
Deposited Residue Count: 239
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	239	Aequorea victoria	Mutation(s): 6 Gene Names: GFP
UniProt
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 Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYS Query on GYS	A	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₅		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.237 (Depositor), 0.179 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.456	α = 90
b = 71.028	β = 90
c = 76.894	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2014-03-05
Changes: Structure summary
Version 1.2: 2017-06-21
Changes: Database references, Source and taxonomy
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references
Version 2.1: 2024-11-27
Changes: Structure summary
Version 3.0: 2026-03-18
Changes: Polymer sequence

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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.