6UY5 | pdb_00006uy5

E. coli cysteine desulfurase SufS with a spontaneously rotated beta-hairpin

• PDB DOI: https://doi.org/10.2210/pdb6UY5/pdb

• Classification: Lyase, Transferase
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-11 Released: 2020-03-25 
• Deposition Author(s): Dunkle, J.A., Frantom, P.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases

Dunkle, J.A., Bruno, M.R., Frantom, P.A.

(2020) Acta Crystallogr D Biol Crystallogr 76: 291-301

• DOI: https://doi.org/10.1107/S2059798320000790

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: 89.52 kDa 
• Atom Count: 6,548 
• Modeled Residue Count: 804 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A, B	406	Escherichia coli K-12	Mutation(s): 0  Gene Names: sufS, csdB, ynhB, b1680, JW1670 EC: 2.8.1.7 (PDB Primary Data), 4.4.1.16 (PDB Primary Data), 3.13.1 (UniProt)
UniProt
Find proteins for P77444 (Escherichia coli (strain K12)) Explore P77444  Go to UniProtKB:  P77444

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.54	α = 90
b = 115.74	β = 114.47
c = 63.66	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Dunkle, J.A., Frantom, P.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM112919

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection