3VYG | pdb_00003vyg

Crystal structure of Thiocyanate hydrolase mutant R136W

• PDB DOI: https://doi.org/10.2210/pdb3VYG/pdb

• Classification: HYDROLASE
• Organism(s): Thiobacillus thioparus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-25 Released: 2013-11-13 
• Deposition Author(s): Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase

Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

To be published.

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: 241.72 kDa 
• Atom Count: 17,343 
• Modeled Residue Count: 1,952 
• Deposited Residue Count: 2,104 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocyanate hydrolase subunit alpha	A, D, G, J	126	Thiobacillus thioparus	Mutation(s): 0  Gene Names: scnA 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 subunit beta	B, E, H, K	157	Thiobacillus thioparus	Mutation(s): 0  Gene Names: scnB 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 subunit gamma	C, F, I, L	243	Thiobacillus thioparus	Mutation(s): 1  Gene Names: scnC 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
TLA	N [auth C], P [auth F], R [auth I], T [auth L]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
3CO	M [auth C], O [auth F], Q [auth I], S [auth L]	COBALT (III) ION Co JAWGVVJVYSANRY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	C, F, I, L	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSO	C, F, I, L	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.448	α = 90
b = 172.398	β = 90
c = 172.531	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-13 
Deposition Author(s): Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Structure summary