3D1P | pdb_00003d1p

Atomic resolution structure of uncharacterized protein from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3D1P/pdb

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


• Deposited: 2008-05-06 Released: 2008-07-08 
• Deposition Author(s): Nocek, B., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.124 (Depositor), 0.126 (DCC) 
• R-Value Work: 
  0.108 (Depositor), 0.111 (DCC) 
• R-Value Observed: 
  0.109 (Depositor) 

Literature

Atomic resolution structure of uncharacterized protein from Saccharomyces cerevisiae.

Nocek, B., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.71 kDa 
• Atom Count: 1,351 
• Modeled Residue Count: 120 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thiosulfate sulfurtransferase YOR285W	A	139	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: YOR285W EC: 2.8.1.1 (PDB Primary Data), 2.8.1 (UniProt)
UniProt
Find proteins for Q12305 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12305  Go to UniProtKB:  Q12305

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.124 (Depositor), 0.126 (DCC) 
• R-Value Work:  0.108 (Depositor), 0.111 (DCC) 
• R-Value Observed: 0.109 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.343	α = 90
b = 37.429	β = 108.86
c = 52.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
ARP/wARP	model building
MLPHARE	phasing
CCP4	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Nocek, B., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary