6JZW | pdb_00006jzw

Crystal structure of SufU from Bacillus subtilis with Cys persulfurated

• PDB DOI: https://doi.org/10.2210/pdb6JZW/pdb

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


• Deposited: 2019-05-04 Released: 2020-05-06 
• Deposition Author(s): Fujishiro, T., Takahashi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.257 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Cysteine-Persulfide Sulfane Sulfur-Ligated Zn Complex of Sulfur-Carrying SufU in the SufCDSUB System for Fe-S Cluster Biosynthesis.

Terahata, T., Shimada, Y., Maki, C., Muroga, S., Sakurai, R., Kunichika, K., Fujishiro, T.

(2024) Inorg Chem 

• DOI: https://doi.org/10.1021/acs.inorgchem.4c02654

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.35 kDa 
• Atom Count: 4,268 
• Modeled Residue Count: 554 
• Deposited Residue Count: 620 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent sulfurtransferase SufU	A, B	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
Zinc-dependent sulfurtransferase SufU	C, D	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	C, D	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.257 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.69	α = 90
b = 35.52	β = 96.41
c = 105.22	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Fujishiro, T., Takahashi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17K14510

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Database references, Structure summary