32JN | pdb_000032jn

Structure of the pathogenic variant P157S of Human SHMT2 in the apo open dimeric conformation

• PDB DOI: https://doi.org/10.2210/pdb32JN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2026-07-13 Released: 2026-09-02 
• Deposition Author(s): Giardina, G., Boumis, G., Di Matteo, A., Breccia, S.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structural and functional defects of mitochondrial serine hydroxymethyltransferase genetic variants responsible for a novel neurodevelopmental syndrome

Giardina, G., Boumis, G., Di Matteo, A., Breccia, S.

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.

Macromolecule Content 

• Total Structure Weight: 53.8 kDa 
• Atom Count: 3,300 
• Modeled Residue Count: 429 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	A	486	Homo sapiens	Mutation(s): 1  Gene Names: SHMT2 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34897 (Homo sapiens) Explore P34897  Go to UniProtKB:  P34897
PHAROS:  P34897 GTEx:  ENSG00000182199

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.716	α = 90
b = 74.153	β = 108.9
c = 74.349	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Giardina, G., Boumis, G., Di Matteo, A., Breccia, S.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	MX-2363

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release