8IYT

Crystal Structure of Serine Palmitoyltransferase complexed with D-methylserine

• PDB DOI: https://doi.org/10.2210/pdb8IYT/pdb

• Classification: TRANSFERASE
• Organism(s): Sphingobacterium multivorum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-06 Released: 2024-04-10 
• Deposition Author(s): Takahashi, A., Murakami, T., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.173 

Literature

Crystal structure of Serine Palmitoyltransferase from Sphingobacterium multivorum

Murakami, T., Takahashi, A., Kayatama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T.

To be published.

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: 44.42 kDa 
• Atom Count: 3,599 
• Modelled Residue Count: 394 
• Deposited Residue Count: 399 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine palmitoyltransferase	A	399	Sphingobacterium multivorum	Mutation(s): 0  Gene Names: spt, I6J33_20140, NCTC11343_02561, SPHINGO8BC_150128 EC: 2.3.1.50
UniProt
Find proteins for A7BFV6 (Sphingobacterium multivorum) Explore A7BFV6  Go to UniProtKB:  A7BFV6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S5R (Subject of Investigation/LOI)	B [auth A]	(2~{R})-2-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid C12 H19 N2 O8 P FVZJSLHHGJVQIU-GFCCVEGCSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.173 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.843	α = 90
b = 61.843	β = 90
c = 208.344	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Takahashi, A., Murakami, T., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release