Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37.52 kDa 
• Atom Count: 2784 
• Modelled Residue Count: 304 
• Deposited Residue Count: 327 
• Unique protein chains: 1

3UTN

Crystal structure of Tum1 protein from Saccharomyces cerevisiae

• PDB DOI: 10.2210/pdb3UTN/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-26 Released: 2012-10-17 
• Deposition Author(s): Qiu, R., Wang, F., Liu, M., Ji, C., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Crystal structure of the Tum1 protein from the yeast Saccharomyces cerevisiae.

Qiu, R., Wang, F., Liu, M., Lou, T., Ji, C.

(2012) Protein Pept Lett 19: 1139-1143

• PubMed: 22587783 
• DOI: 10.2174/092986612803217060
• Primary Citation of Related Structures:  
  3UTN


• PubMed Abstract: 
  

Yeast tRNA-thiouridine modification protein 1 (Tum1) plays essential role in the sulfur transfer process of Urm1 system, which in turn is involved in many important cellular processes. In the rhodanese-like domain (RLD), conserved cysteine residue is proved to be the centre of active site of sulfurtransferases and crucial for the substrate recognition. In this report, we describe the crystal structure of Tum1 protein at 1.90 A resolution which, despite consisting of two RLDs, has only one conserved cysteine residue in the C-terminal RLD. An unaccounted electron density is found near the active site, which might point to the new cofactor in the sulfur transfer mechanism.

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Organizational Affiliation: 

State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiosulfate sulfurtransferase TUM1	A [auth X]	327	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TUM1, YOR251C EC: 2.8.1.1
UniProt
Find proteins for Q08686 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08686  Go to UniProtKB:  Q08686

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	B [auth X], C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], J [auth X]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.228 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.939	α = 90
b = 120.939	β = 90
c = 48.354	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-26 
• Released Date: 2012-10-17 
Deposition Author(s): Qiu, R., Wang, F., Liu, M., Ji, C., Gong, W.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references, Derived calculations