7XEL

SufS soaked with D-penicillamine

• PDB DOI: https://doi.org/10.2210/pdb7XEL/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-31 Released: 2023-04-05 
• Deposition Author(s): Nakamura, R., Fujishiro, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.188 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Literature

X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine

Nakamura, R., Takahashi, Y., Fujishiro, T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.24 kDa 
• Atom Count: 3,549 
• Modelled Residue Count: 405 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase SufS	A	419	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: sufS, csd, yurW, BSU32690 EC: 2.8.1.7
UniProt
Find proteins for O32164 (Bacillus subtilis (strain 168)) Explore O32164  Go to UniProtKB:  O32164

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.188 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93	α = 90
b = 93	β = 90
c = 129	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Nakamura, R., Fujishiro, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K19340

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description