2EG4 | pdb_00002eg4

Crystal Structure of Probable Thiosulfate Sulfurtransferase

• PDB DOI: https://doi.org/10.2210/pdb2EG4/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-27 Released: 2008-03-04 
• Deposition Author(s): Sakai, H., Ebihara, A., Kitamura, Y., Shinkai, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Probable Thiosulfate Sulfurtransferase

Sakai, H., Ebihara, A., Kitamura, Y., Shinkai, A., Kuramitsu, S., Yokoyama, S.

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.01 kDa 
• Atom Count: 4,050 
• Modeled Residue Count: 459 
• Deposited Residue Count: 460 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thiosulfate sulfurtransferase	A	230	Thermus thermophilus HB8	Mutation(s): 0  EC: 2.8.1
UniProt
Find proteins for Q5SHV8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHV8  Go to UniProtKB:  Q5SHV8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thiosulfate sulfurtransferase	B	230	Thermus thermophilus HB8	Mutation(s): 0  EC: 2.8.1
UniProt
Find proteins for Q5SHV8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHV8  Go to UniProtKB:  Q5SHV8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.694	α = 90
b = 71.218	β = 90
c = 115.483	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Sakai, H., Ebihara, A., Kitamura, Y., Shinkai, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary