8FZW | pdb_00008fzw

Thaumatin crystallized in cyclic olefin copolymer-based microfluidic chips

• PDB DOI: https://doi.org/10.2210/pdb8FZW/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Expression System: Thaumatococcus daniellii
• Mutation(s): No 


• Deposited: 2023-01-30 Released: 2023-10-18 
• Deposition Author(s): Liu, Z., Gu, K., Shelby, M.L., Gilbile, D., Lyubimov, A.Y., Russi, S., Cohen, A.E., Coleman, M.A., Frank, M., Kuhl, T.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.

Liu, Z., Gu, K.K., Shelby, M.L., Gilbile, D., Lyubimov, A.Y., Russi, S., Cohen, A.E., Narayanasamy, S.R., Botha, S., Kupitz, C., Sierra, R.G., Poitevin, F., Gilardi, A., Lisova, S., Coleman, M.A., Frank, M., Kuhl, T.L.

(2023) Acta Crystallogr D Struct Biol 79: 944-952

• PubMed: 37747292 
• DOI: https://doi.org/10.1107/S2059798323007027
• Primary Citation Related Structures: 
  8FZW, 8SCY, 8SIL


• PubMed Abstract: 
  

  Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.

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Organizational Affiliation: 
• Department of Chemical Engineering, University of California at Davis, Davis, CA 95616, USA.
Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

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: 22.39 kDa 
• Atom Count: 1,751 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.666	α = 90
b = 58.666	β = 90
c = 151.557	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Liu, Z., Gu, K., Shelby, M.L., Gilbile, D., Lyubimov, A.Y., Russi, S., Cohen, A.E., Coleman, M.A., Frank, M., Kuhl, T.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary