6C5Y | pdb_00006c5y

Crystal structure of thaumatin from microcrystals

• PDB DOI: https://doi.org/10.2210/pdb6C5Y/pdb

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


• Deposited: 2018-01-17 Released: 2018-05-30 
• Deposition Author(s): Guo, G., Fuchs, M., Shi, W., Skinner, J., Berman, E., Ogata, C.M., Hendrickson, W.A., McSweeney, S., Liu, Q.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.220 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Sample manipulation and data assembly for robust microcrystal synchrotron crystallography.

Guo, G., Fuchs, M.R., Shi, W., Skinner, J., Berman, E., Ogata, C.M., Hendrickson, W.A., McSweeney, S., Liu, Q.

(2018) IUCrJ 5: 238-246

• PubMed: 29755741 
• DOI: https://doi.org/10.1107/S2052252518005389
• Primary Citation Related Structures: 
  6C5Y


• PubMed Abstract: 
  

  With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallo-graphy with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described. The method demonstrates that microcrystals may be routinely utilized for the acquisition and assembly of complete data sets from synchrotron microdiffraction beamlines.

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Organizational Affiliation: 
• Photon Science Directorate, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA.
Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
GM/CA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, 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: 22.23 kDa 
• Atom Count: 1,669 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.220 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.576	α = 90
b = 57.576	β = 90
c = 150.477	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Guo, G., Fuchs, M., Shi, W., Skinner, J., Berman, E., Ogata, C.M., Hendrickson, W.A., McSweeney, S., Liu, Q.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107462

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary