6TI4 | pdb_00006ti4

SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/D-Serine/Lys230 gem diamine complex

• PDB DOI: https://doi.org/10.2210/pdb6TI4/pdb

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


• Deposited: 2019-11-21 Released: 2020-04-15 
• 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: 1.93 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Y55S Serine Hydroxymethyltransferase variant from Streptococcus thermophilus in complex with gem-diamine intermediate of D-serine

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: 91 kDa 
• Atom Count: 6,818 
• Modeled 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 Q5M4W1 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4W1  Go to UniProtKB:  Q5M4W1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O3Z (Subject of Investigation/LOI)	D [auth A], G [auth C]	(2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid C11 H17 N2 O8 P ODVKKQWXKRZJLG-SECBINFHSA-N
GOL (Subject of Investigation/LOI)	C [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.782	α = 90
b = 114.782	β = 90
c = 192.833	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: 2020-04-15 
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: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description