5XT5

SufS-SufU complex from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb5XT5/pdb

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


• Deposited: 2017-06-17 Released: 2017-12-20 
• Deposition Author(s): Fujishiro, T., Takahashi, Y.
• Funding Organization(s): JSPS, Sumitomo Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.243 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Models: experimental

Literature

Zinc-Ligand Swapping Mediated Complex Formation and Sulfur Transfer between SufS and SufU for Iron-Sulfur Cluster Biogenesis in Bacillus subtilis

Fujishiro, T., Terahata, T., Kunichika, K., Yokoyama, N., Maruyama, C., Asai, K., Takahashi, Y.

(2017) J Am Chem Soc 139: 18464-18467

• PubMed: 29235855 
• DOI: https://doi.org/10.1021/jacs.7b11307
• Primary Citation of Related Structures:  
  5XT5, 5XT6


• PubMed Abstract: 
  

  SufU is a zinc-containing protein involved in mobilization of sulfur from SufS for iron-sulfur cluster biogenesis of Bacillus subtilis. Structural basis for the sulfur transfer in SufS-SufU complex was revealed. A zinc-ligand exchange reaction upon SufS-SufU complexation provides a free thiol from Cys41 of SufU as a sulfur acceptor.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University , Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 128.31 kDa 
• Atom Count: 8,619 
• Modelled Residue Count: 1,082 
• Deposited Residue Count: 1,148 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent sulfurtransferase SufU	A [auth D], D [auth C]	155	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: sufU, iscU, nifU, yurV, BSU32680 EC: 2
UniProt
Find proteins for O32163 (Bacillus subtilis (strain 168)) Explore O32163  Go to UniProtKB:  O32163

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase SufS	B [auth A], C [auth B]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	F [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ZN	E [auth D], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.243 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.98	α = 90
b = 74.98	β = 90
c = 364.41	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: 2017-12-20 
Deposition Author(s): Fujishiro, T., Takahashi, Y.

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Funding Organization	Location	Grant Number
JSPS	Japan	15H04472
JSPS	Japan	17K14510
Sumitomo Foundation	Japan	163037

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description