6SZZ | pdb_00006szz

Crystal structure of Cold Shock Protein B (CspB) containing the modified residue 4-F-Trp

• PDB DOI: https://doi.org/10.2210/pdb6SZZ/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-02 Released: 2020-02-26 
• Deposition Author(s): Zhou, T., Mayans, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.231 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein.

Welte, H., Zhou, T., Mihajlenko, X., Mayans, O., Kovermann, M.

(2020) Sci Rep 10: 2640-2640

• PubMed: 32060391 
• DOI: https://doi.org/10.1038/s41598-020-59446-w
• Primary Citation Related Structures: 
  6SZZ, 6T00


• PubMed Abstract: 
  

  Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.

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Organizational Affiliation: 
• Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.
Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.
Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.
Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. [e-mail].
Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. [e-mail].
Zukunftskolleg, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 7.57 kDa 
• Atom Count: 548 
• Modeled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold shock protein CspD	A	67	Bacillus subtilis	Mutation(s): 0  Gene Names: B4122_0412, B4417_4327, CJ481_22435, DFO69_3150, ETA10_05025, ETK61_05130, ETL41_18150, FA024_03420, SC09_Contig19orf00064
UniProt
Find proteins for P32081 (Bacillus subtilis (strain 168)) Explore P32081  Go to UniProtKB:  P32081

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4FW	A	L-PEPTIDE LINKING	C11 H11 F N2 O2		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.231 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.05	α = 90
b = 56.05	β = 90
c = 55.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Zhou, T., Mayans, O.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description