Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.84 kDa 
• Atom Count: 3962 
• Residue Count: 452 
• Unique protein chains: 1

6AA7

Fluorescent protein from Acropora digitifera

• DOI: 10.2210/pdb6AA7/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Acropora digitifera
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-07-17 Released: 2018-08-22 
• Deposition Author(s): Kim, S.E., Hwang, K.Y., Nam, K.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Spectral and structural analysis of a red fluorescent protein from Acropora digitifera.

Kim, S.E., Hwang, K.Y., Nam, K.H.

(2019) Protein Sci 28: 375-381

• PubMed: 30368951 
• DOI: 10.1002/pro.3540
• Primary Citation of Related Structures:  
  6AA7


• PubMed Abstract: 
  

Fluorescent proteins (FPs) possess a wide variety of spectral properties that make them of widespread interest as optical markers. These proteins can be applied as pH indicators or metal biosensors. The discovery and characterization of new fluorescent proteins is expected to further extend their application. Here, we report the spectral and structural analysis of a red fluorescent protein from Acropora digitifera (designated AdRed). This protein shows a tetrameric state and is red emitting, with excitation and emission maxima at 567 and 612 nm, respectively. Its crystal structure shows the tetrameric interface stabilized by hydrogen bonding and salt bridges. The electron density map of the chromophore, consisting of Asp66-Tyr67-Gly68, shows the decarboxylated side chain of Asp66. Ser223, located near the chromophore, has the role of bridging His202 and Glu221, and is part of the hydrogen bond network. Mutated AdRed with Cys148Ser reveals a blue shift in fluorescence excitation and emission. Our results provide insights into understanding the molecular function of AdRed and other FPs.

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Organizational Affiliation: 

Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescent protein	A, B	233	Acropora digitifera	Mutation(s): 1  Gene Names: M, LWE
Find proteins for A0A1S7IWI8 (Acropora digitifera) Explore A0A1S7IWI8  Go to UniProtKB:  A0A1S7IWI8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
XYG	A,B	L-PEPTIDE LINKING	C14 H13 N3 O4		ASP, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.618	α = 90
b = 90.553	β = 90
c = 73.429	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-17 
• Released Date: 2018-08-22 
Deposition Author(s): Kim, S.E., Hwang, K.Y., Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History 

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references