2V4E | pdb_00002v4e

A non-cytotoxic DsRed variant for whole-cell labeling

• PDB DOI: https://doi.org/10.2210/pdb2V4E/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Discosoma sp.
• Expression System: Escherichia coli str. K-12 substr. DH10B
• Mutation(s): No 


• Deposited: 2008-09-20 Released: 2008-11-04 
• Deposition Author(s): Strack, R.L., Strongin, D.E., Bhattacharyya, D., Tao, W., Berman, A., Broxmeyer, H.E., Keenan, R.J., Glick, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

A Noncytotoxic Dsred Variant for Whole-Cell Labeling.

Strack, R.L., Strongin, D.E., Bhattacharyya, D., Tao, W., Berman, A., Broxmeyer, H.E., Keenan, R.J., Glick, B.S.

(2008) Nat Methods 5: 955

• PubMed: 18953349 
• DOI: https://doi.org/10.1038/nmeth.1264
• Primary Citation of Related Structures:  
  2V4E


• PubMed Abstract: 
  

  A common application of fluorescent proteins is to label whole cells, but many RFPs are cytotoxic when used with standard high-level expression systems. We engineered a rapidly maturing tetrameric fluorescent protein called DsRed-Express2 that has minimal cytotoxicity. DsRed-Express2 exhibits strong and stable expression in bacterial and mammalian cells, and it outperforms other available RFPs with regard to photostability and phototoxicity.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center W238, Chicago, Illinois 60637, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 201.43 kDa 
• Atom Count: 14,705 
• Modelled Residue Count: 1,742 
• Deposited Residue Count: 1,744 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RED FLUORESCENT PROTEIN DRFP583	A	218	Discosoma sp.	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RED FLUORESCENT PROTEIN DRFP583	B	218	Discosoma sp.	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RED FLUORESCENT PROTEIN DRFP583	C, D, E, F, G, H	218	Discosoma sp.	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.526	α = 90
b = 122.619	β = 90
c = 164.851	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Strack, R.L., Strongin, D.E., Bhattacharyya, D., Tao, W., Berman, A., Broxmeyer, H.E., Keenan, R.J., Glick, B.S.

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description