7AT6 | pdb_00007at6

Structure of thaumatin collected by femtosecond serial crystallography on a COC membrane

• PDB DOI: https://doi.org/10.2210/pdb7AT6/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-29 Released: 2021-11-24 
• Deposition Author(s): Martiel, I., Marsh, M., Vera, L., Huang, C.Y., Olieric, V., Leonarski, P., Nass, K., Padeste, C., Karpik, A., Wang, M., Pedrini, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Commissioning results from the SwissMX instrument for fixed target macromolecular crystallography at SwissFEL

Martiel, I., Pradervand, C., Panepucci, E., Zamofing, T., Nass, K., Marsh, M., Vera, L., Hunag, C.Y., Olieric, V., Buntschu, D., Kaelin, R., Leonarski, P., Ozerov, D., Padeste, C., Karpik, A., Thominet, V., Hora, J., Olieric, N., Weinert, T., Wranik, M., Brunle, S., Standfuss, J., Aurelius, O., John, J., Hogbom, M., Zhang, L., Einsle, O., Papp, G., Basu, S., Cipriani, F., Beaud, P., Mankowsky, R., Glettig, W., Mozzanica, A., Redford, S., Schmidt, B., Bunk, O., Abela, R., Wang, M., Lemke, H., Pedrini, B.

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: 22.95 kDa 
• Atom Count: 1,823 
• Modeled Residue Count: 206 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A], C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
PGR	D [auth A], E [auth A], F [auth A], G [auth A]	R-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-GSVOUGTGSA-N
NA	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.6	α = 90
b = 58.6	β = 90
c = 151.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Martiel, I., Marsh, M., Vera, L., Huang, C.Y., Olieric, V., Leonarski, P., Nass, K., Padeste, C., Karpik, A., Wang, M., Pedrini, B.

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary