9CE6

Key structural role for the conserved cis-proline of soybean serine hydroxymethyltransferase

• PDB DOI: https://doi.org/10.2210/pdb9CE6/pdb

• Classification: TRANSFERASE
• Organism(s): Glycine max
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-26 Released: 2024-10-16 
• Deposition Author(s): Beamer, L.J., Samarakoon, V.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institute of Food and Agriculture (NIFA, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.256 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Key structural role of a conserved cis-proline revealed by the P285S variant of soybean serine hydroxymethyltransferase 8

Samarakoon, V., Owuocha, L.F., Hammond, J., Mitchum, M.G., Beamer, L.J.

(2024) Biochem J 

• DOI: https://doi.org/10.1042/BCJ20240338

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 108.72 kDa 
• Atom Count: 7,036 
• Modelled Residue Count: 902 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	492	Glycine max	Mutation(s): 0  Gene Names: SHMT EC: 2.1.2.1
UniProt
Find proteins for K4FZF8 (Glycine max) Explore K4FZF8  Go to UniProtKB:  K4FZF8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.256 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.603	α = 90
b = 129.685	β = 90
c = 58.629	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Beamer, L.J., Samarakoon, V.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	IOS 2152548
National Institute of Food and Agriculture (NIFA, United States)	United States	NIFA 2021-67013-35887

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release