1U83 | pdb_00001u83

PSL synthase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1U83/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2004-08-04 Released: 2004-09-14 
• Deposition Author(s): Cuff, M.E., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

PSL synthase from Bacillus subtilis

Cuff, M.E., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A.

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: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 31.75 kDa 
• Atom Count: 2,013 
• Modeled Residue Count: 225 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphosulfolactate synthase	A	276	Bacillus subtilis	Mutation(s): 3  Gene Names: comA EC: 4.4.1.19
UniProt
Find proteins for O06739 (Bacillus subtilis (strain 168)) Explore O06739  Go to UniProtKB:  O06739

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 2.20 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.071	α = 90
b = 92.071	β = 90
c = 92.071	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-2000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	model building
CNS	refinement
HKL-2000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-14 
Deposition Author(s): Cuff, M.E., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-09-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2012-09-26
  Changes: Structure summary
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary