2DD4

Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme

• PDB DOI: https://doi.org/10.2210/pdb2DD4/pdb

• Classification: HYDROLASE
• Organism(s): Thiobacillus thioparus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-19 Released: 2007-01-30 
• Deposition Author(s): Arakawa, T., Kawano, Y., Kataoka, S., Katayama, Y., Kamiya, N., Yohda, M., Odaka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 243.22 kDa 
• Atom Count: 18,077 
• Modelled Residue Count: 1,954 
• Deposited Residue Count: 2,104 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocyanate hydrolase alpha subunit	A, D, G, J	126	Thiobacillus thioparus	Mutation(s): 0  EC: 3.5.5.8
UniProt
Find proteins for O66187 (Thiobacillus thioparus) Explore O66187  Go to UniProtKB:  O66187

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocyanate hydrolase beta subunit	B, E, H, K	157	Thiobacillus thioparus	Mutation(s): 0  EC: 3.5.5.8
UniProt
Find proteins for O66186 (Thiobacillus thioparus) Explore O66186  Go to UniProtKB:  O66186

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocyanate hydrolase gamma subunit	C, F, I, L	243	Thiobacillus thioparus	Mutation(s): 0  EC: 3.5.5.8
UniProt
Find proteins for O66188 (Thiobacillus thioparus) Explore O66188  Go to UniProtKB:  O66188

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRU	M [auth B], N [auth B], O [auth C], T [auth H], U [auth H], V [auth H], Y [auth K], Z [auth K]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
TLA	AA [auth L], BA [auth L], P [auth C], Q [auth C], R [auth F], S [auth F], W [auth I], X [auth I]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.307	α = 90
b = 175.602	β = 90
c = 114.791	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Arakawa, T., Kawano, Y., Kataoka, S., Katayama, Y., Kamiya, N., Yohda, M., Odaka, M.

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-07-10
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 2.2: 2024-03-13
  Changes: Data collection, Database references, Structure summary