5MJG | pdb_00005mjg

Single-shot pink beam serial crystallography: Thaumatin

• PDB DOI: https://doi.org/10.2210/pdb5MJG/pdb

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


• Deposited: 2016-12-01 Released: 2017-12-20 
• Deposition Author(s): Meents, A., Oberthuer, D., Lieske, J., Srajer, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Single-shot pink beam serial crystallography: Thaumatin

Meents, A., Oberthuer, D., Lieske, J., Srajer, V.

To be published.

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: 22.4 kDa 
• Atom Count: 1,740 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	B [auth A]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.4	α = 90
b = 58.4	β = 90
c = 152.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Epinorm	data reduction
Precognition	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Meents, A., Oberthuer, D., Lieske, J., Srajer, V.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary