6TGH

SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex

• PDB DOI: https://doi.org/10.2210/pdb6TGH/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus thermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-11-15 Released: 2020-06-03 
• Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.284 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus

Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 181.22 kDa 
• Atom Count: 12,968 
• Modelled Residue Count: 1,640 
• Deposited Residue Count: 1,660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B [auth C], C [auth B], D	415	Streptococcus thermophilus	Mutation(s): 1  Gene Names: glyA, CDA68_00974, DID82_07515 EC: 2.1.2.1
UniProt
Find proteins for Q5M0B4 (Streptococcus thermophilus (strain CNRZ 1066)) Explore Q5M0B4  Go to UniProtKB:  Q5M0B4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVM (Subject of Investigation/LOI)	F [auth A], K [auth B]	L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene] C11 H14 N2 O8 P JFLJYKRWFQAEDK-QLKAYGNNSA-N
PLP (Subject of Investigation/LOI)	I [auth C], M [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
DSN (Subject of Investigation/LOI)	H [auth C], L [auth D]	D-SERINE C3 H7 N O3 MTCFGRXMJLQNBG-UWTATZPHSA-N
NA (Subject of Investigation/LOI)	E [auth A], G [auth C], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.284 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.795	α = 90
b = 112.93	β = 93.1
c = 131.918	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description