6FJ9 | pdb_00006fj9

Structure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV.

• PDB DOI: https://doi.org/10.2210/pdb6FJ9/pdb

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


• Deposited: 2018-01-21 Released: 2018-01-31 
• Deposition Author(s): McCarthy, A.A., Mueller-Dieckmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.

McCarthy, A.A., Barrett, R., Beteva, A., Caserotto, H., Dobias, F., Felisaz, F., Giraud, T., Guijarro, M., Janocha, R., Khadrouche, A., Lentini, M., Leonard, G.A., Lopez Marrero, M., Malbet-Monaco, S., McSweeney, S., Nurizzo, D., Papp, G., Rossi, C., Sinoir, J., Sorez, C., Surr, J., Svensson, O., Zander, U., Cipriani, F., Theveneau, P., Mueller-Dieckmann, C.

(2018) J Synchrotron Radiat 25: 1249-1260

• PubMed: 29979188 
• DOI: https://doi.org/10.1107/S1600577518007166
• Primary Citation Related Structures: 
  6FID, 6FJ2, 6FJ4, 6FJ6, 6FJ8, 6FJ9


• PubMed Abstract: 
  

  ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France.
European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France.

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: 22.38 kDa 
• Atom Count: 1,725 
• Modeled Residue Count: 206 
• 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

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: 1.50 Å
• R-Value Free:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/547

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.57	α = 90
b = 58.57	β = 90
c = 151.544	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): McCarthy, A.A., Mueller-Dieckmann, C.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2018-08-08
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary