5XT5 | pdb_00005xt5

SufS-SufU complex from Bacillus subtilis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1021/jacs.7b11307
  • Primary Citation 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.

    • 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.

Macromolecule Content 

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

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc-dependent sulfurtransferase SufUA [auth D],
D [auth C]		155Bacillus subtilis subsp. subtilis str. 168Mutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32163
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine desulfurase SufSB [auth A],
C [auth B]		419Bacillus subtilis subsp. subtilis str. 168Mutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32164
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.98α = 90
b = 74.98β = 90
c = 364.41γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JSPSJapan15H04472
JSPSJapan17K14510
Sumitomo FoundationJapan163037

Revision History  (Full details and data files)

  • 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