2WHS

Fluorescent Protein mKeima at pH 3.8

PDB DOI: https://doi.org/10.2210/pdb2WHS/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Montipora sp. 20
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-05-06 Released: 2009-08-11
Deposition Author(s): Violot, S., Carpentier, P., Blanchoin, L., Bourgeois, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.248
R-Value Work: 0.190
R-Value Observed: 0.193

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Reverse Ph-Dependence of Chromophore Protonation Explains the Large Stokes Shift of the Red Fluorescent Protein Mkeima.

Violot, S., Carpentier, P., Blanchoin, L., Bourgeois, D.

(2009) J Am Chem Soc 131: 10356

PubMed: 19722611 Search on PubMed
DOI: https://doi.org/10.1021/ja903695n
Primary Citation of Related Structures:
2WHS, 2WHT, 2WHU

PubMed Abstract:
The recently developed red fluorescent protein Keima exhibits the largest Stokes shift (180 nm) observed to date. Combining X-ray crystallography with (in crystallo) UV-visible absorption, fluorescence, and Raman spectroscopy, we have investigated molecular determinants of this peculiar property. The results demonstrate a pH-dependent "reverse chromophore protonation" triggered by the key residue Asp157 and which couples to cis/trans isomerization of the chromophore. These data provided guidelines to rationally design a useful Keima variant.

Organizational Affiliation

Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire Végétale, CEA, CNRS, INRA, Université Joseph Fourier, 17 rue des Martyrs, F-38054 Grenoble, France.

Macromolecule Content

Total Structure Weight: 109.98 kDa
Atom Count: 7,919
Modelled Residue Count: 887
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LARGE STOKES SHIFT FLUORESCENT PROTEIN	A, B, C, D	240	Montipora sp. 20	Mutation(s): 1
UniProt
Find proteins for Q1JV70 (Montipora sp. 20) Explore Q1JV70 Go to UniProtKB: Q1JV70
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1JV70
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.248
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.57	α = 90
b = 98.1	β = 90
c = 123.27	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2012-07-04
Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
Version 1.2: 2018-03-07
Changes: Source and taxonomy
Version 1.3: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation
Version 1.4: 2019-10-23
Changes: Data collection, Database references, Other
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2023-12-13
Changes: Refinement description