7F8E | pdb_00007f8e

Crystal structure of YggS from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb7F8E/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2021-07-02 Released: 2022-01-12 
• Deposition Author(s): Wang, L., Chen, Y., Bu, T., Bai, X.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of YggS from Fusobacterium nucleatum

Wang, L., Chen, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.92 kDa 
• Atom Count: 6,056 
• Modelled Residue Count: 665 
• Deposited Residue Count: 669 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal phosphate homeostasis protein	A, B, C	223	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0  Gene Names: FN0561
UniProt
Find proteins for Q8RFW9 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RFW9  Go to UniProtKB:  Q8RFW9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.929	α = 90
b = 146.375	β = 93.355
c = 74.128	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Wang, L., Chen, Y., Bu, T., Bai, X.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087
National Research Foundation (NRF, Korea)	Korea, Republic Of	2017M3A9F6029736

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Structure summary