6Z1Y | pdb_00006z1y

Crystal structure of type-I ribosome-inactivating protein trichobakin (TBK)

• PDB DOI: https://doi.org/10.2210/pdb6Z1Y/pdb

• Classification: HYDROLASE
• Organism(s): Trichosanthes sp. Bac Kan 8-98
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-14 Released: 2020-05-27 
• Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Britikov, V.V., Bocharov, E.V., Britikova, E.V., Le, T.B.T., Phan, C.V., Popov, V.O., Usanov, S.A.
• Funding Organization(s): Russian Science Foundation, Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of type-I ribosome-inactivating protein trichobakin (TBK)

Britikov, V.V., Britikova, E.V., Bocharov, E.V., Le, T.B.T., Phan, C.V., Nikolaeva, A.Y., Boyko, K.M., Arseniev, A.S., Usanov, S.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 109.56 kDa 
• Atom Count: 8,335 
• Modeled Residue Count: 981 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trichobakin	A, B, C, D	248	Trichosanthes sp. Bac Kan 8-98	Mutation(s): 0  Gene Names: TBK EC: 3.2.2.22
UniProt
Find proteins for Q9LRE3 (Trichosanthes sp. Bac Kan 8-98) Explore Q9LRE3  Go to UniProtKB:  Q9LRE3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth B], G [auth B], H [auth C], I [auth C], J [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.72	α = 90
b = 73.73	β = 96.85
c = 88.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Britikov, V.V., Bocharov, E.V., Britikova, E.V., Le, T.B.T., Phan, C.V., Popov, V.O., Usanov, S.A.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	19-74-30014
Not funded	Belarus	BRFFR-VAST X17B-012

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description