6KZW | pdb_00006kzw

Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb6KZW/pdb

• Classification: PROTEIN BINDING
• Organism(s): Fusobacterium nucleatum subsp. nucleatum
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-09-25 Released: 2019-10-16 
• Deposition Author(s): Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.217 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from Fusobacterium nucleatum

Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, 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: homology

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: 6,055 
• Modeled 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	Mutation(s): 2  Gene Names: RO03_02185
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
PO4 (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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:  0.217 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.181 (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: 2019-10-16 
Deposition Author(s): Chen, Y., Wang, L., Shang, F., Lan, J., Liu, W., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Derived calculations
• Version 1.2: 2021-01-13
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary