5YT1 | pdb_00005yt1

Crystal structrure of near infrared fluoresecent protein mNeptune684

• PDB DOI: https://doi.org/10.2210/pdb5YT1/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Entacmaea quadricolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-11-21 
• Deposition Author(s): Zhang, X.E., Wang, D.B., Yuan, Y., Li, D.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structrure of near infrared fluoresecent protein mNeptune684

Zhang, X.E., Wang, D.B., Yuan, Y., Li, D.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 115.67 kDa 
• Atom Count: 7,994 
• Modeled Residue Count: 905 
• Deposited Residue Count: 1,016 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
near infrared fluoresecent protein mNeptune684	A, B, C, D	254	Entacmaea quadricolor	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A, B, C, D	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.643	α = 90
b = 116.878	β = 106.65
c = 63.721	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Zhang, X.E., Wang, D.B., Yuan, Y., Li, D.F.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2026-03-18
  Changes: Polymer sequence, Structure summary