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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.271 (Depositor), 0.275 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nmeth.1264
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RED FLUORESCENT PROTEIN DRFP583	A	218	Discosoma sp.	Mutation(s): 0
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8 Go to UniProtKB: Q9U6Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9U6Y8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RED FLUORESCENT PROTEIN DRFP583	B	218	Discosoma sp.	Mutation(s): 0
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8 Go to UniProtKB: Q9U6Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9U6Y8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RED FLUORESCENT PROTEIN DRFP583	C, D, E, F, G C, D, E, F, G, H	218	Discosoma sp.	Mutation(s): 0
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8 Go to UniProtKB: Q9U6Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9U6Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ Query on 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), 0.275 (DCC)
R-Value Work: 0.220 (Depositor), 0.223 (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

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Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Revision History (Full details and data files)

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