4JC2 | pdb_00004jc2

Isolation, Cloning and Biophysical Analysis of a Novel Hexameric Green Fluorescent Protein from a Philippine Soft Coral

PDB DOI: https://doi.org/10.2210/pdb4JC2/pdb

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

Deposited: 2013-02-21 Released: 2014-03-19
Deposition Author(s): Huang, Y.C., Emralino, F.L., Liu, F.C., Saloma, C.P., Bascos, N.A., Chen, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.235 (Depositor), 0.236 (DCC)
R-Value Work:
0.175 (Depositor), 0.181 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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This is version 3.0 of the entry. See complete history.

Literature

Isolation, Cloning and Biophysical Analysis of a Novel Hexameric Green Fluorescent Protein from a Philippine Soft Coral

Huang, Y.C., Emralino, F.L., Liu, F.C., Saloma, C.P., Bascos, N.A., Chen, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 154.35 kDa
Atom Count: 11,563
Modeled Residue Count: 1,325
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
asFP504	A, B, C, D, E A, B, C, D, E, F	222	Alcyonium	Mutation(s): 0
UniProt
Find proteins for B5BRC3 (Sarcophyton sp. sesoko01) Explore B5BRC3 Go to UniProtKB: B5BRC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5BRC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ Query on CRQ	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₆ H₁₆ N₄ O₅		GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.235 (Depositor), 0.236 (DCC)
R-Value Work: 0.175 (Depositor), 0.181 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.067	α = 90
b = 127.707	β = 90
c = 158.803	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-03-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-19
Type: Initial release
Version 1.1: 2014-03-26
Changes: Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-10-30
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.