6JZV

Crystal structure of SufU from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb6JZV/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Zinc-persulfide complex for sulfur mobilization by SufU in SUF-like machinery for Fe-S cluster biosynthesis

Fujishiro, T., Terahata, T., Shimada, Y., Takahashi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 69.29 kDa
Atom Count: 4,318
Modelled Residue Count: 557
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent sulfurtransferase SufU	A, B, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32163
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.213
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.32	α = 68.99
b = 54.45	β = 75.86
c = 70.38	γ = 72.54

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.