3PGY

Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant.

• PDB DOI: https://doi.org/10.2210/pdb3PGY/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-11-02 Released: 2010-11-17 
• Deposition Author(s): Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.208 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant

Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A.

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 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: 183.94 kDa 
• Atom Count: 13,941 
• Modelled Residue Count: 1,606 
• Deposited Residue Count: 1,660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C, D	415	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1  Gene Names: glyA EC: 2.1.2.1
UniProt
Find proteins for Q5HE87 (Staphylococcus aureus (strain COL)) Explore Q5HE87  Go to UniProtKB:  Q5HE87

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], G [auth B], H [auth B], I [auth B], L [auth C], O [auth D], P [auth D], Q [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GLY	F [auth A], J [auth B], K [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO	M [auth C], N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.208 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33PGY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.081	α = 90
b = 86.531	β = 90
c = 301.806	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description