6TI1

SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/L-Threonine/Lys230 gem diamine complex

• PDB DOI: https://doi.org/10.2210/pdb6TI1/pdb

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


• Deposited: 2019-11-21 Released: 2020-04-29 
• Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.178 
• R-Value Observed: 0.178 

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

Macromolecule Content

• Total Structure Weight: 90.94 kDa 
• Atom Count: 6,673 
• Modelled Residue Count: 820 
• Deposited Residue Count: 832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B [auth C]	416	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BO (Subject of Investigation/LOI)	D [auth A], F [auth C]	N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine C12 H19 N2 O8 P IZWQBQLGLAKRMN-XCBNKYQSSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.178 
• R-Value Observed: 0.178 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.708	α = 90
b = 114.708	β = 90
c = 192.063	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
XPREP	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	--

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary