2WLR | pdb_00002wlr

Putative thiosulfate sulfurtransferase YnjE

• PDB DOI: https://doi.org/10.2210/pdb2WLR/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-06-25 Released: 2010-09-01 
• Deposition Author(s): Declercq, J.P., Smeets, A., Depuydt, M., Collet, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Structural Analysis of Ynje, a Putative Thiosulfate Sulfurtransferase

Declercq, J.P., Smeets, A., Depuydt, M., Collet, J.F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 48.29 kDa 
• Atom Count: 3,790 
• Modeled Residue Count: 408 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE	A	423	Escherichia coli	Mutation(s): 0  EC: 2.8.1.1
UniProt
Find proteins for P78067 (Escherichia coli (strain K12)) Explore P78067  Go to UniProtKB:  P78067

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A], C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.33	α = 90
b = 84.01	β = 90
c = 132.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Declercq, J.P., Smeets, A., Depuydt, M., Collet, J.F.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2019-03-13
  Changes: Data collection, Derived calculations, Experimental preparation, Other, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary