3SZS | pdb_00003szs

Crystal structure analysis of hellethionin D

• PDB DOI: https://doi.org/10.2210/pdb3SZS/pdb

• Classification: TOXIN
• Organism(s): Helleborus purpurascens
• Mutation(s): No 


• Deposited: 2011-07-19 Released: 2012-07-25 
• Deposition Author(s): Thorn, A., Uson, I., Eduardo, C., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.221 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of Hellethionin D

Thorn, A., Uson, I., Eduardo, C., Sheldrick, G.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

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.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.02 kDa 
• Atom Count: 2,752 
• Modeled Residue Count: 318 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hellethionin-D	A, B, C, D, E, F, G	46	Helleborus purpurascens	Mutation(s): 0
UniProt
Find proteins for P60057 (Helleborus purpurascens) Explore P60057  Go to UniProtKB:  P60057

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	AA [auth E], AB [auth G], BB [auth G], DA [auth E], DB [auth G], FA [auth E], GA [auth E], GB [auth G], H [auth A], HA [auth E], I [auth A], IA [auth E], JA [auth E], KA [auth E], LA [auth E], M [auth A], MA [auth F], N [auth B], OA [auth F], P [auth C], Q [auth C], QA [auth F], R [auth D], RA [auth F], S [auth D], TA [auth F], U [auth D], V [auth E], VA [auth G], W [auth E], WA [auth G], Y [auth E], ZA [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	BA [auth E], CA [auth E], CB [auth G], EA [auth E], EB [auth G], FB [auth G], J [auth A], K [auth A], L [auth A], NA [auth F], O [auth B], PA [auth F], SA [auth F], T [auth D], UA [auth G], X [auth E], XA [auth G], YA [auth G], Z [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.221 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.829	α = 90
b = 129.829	β = 90
c = 103.994	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Thorn, A., Uson, I., Eduardo, C., Sheldrick, G.M.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary