5WCX | pdb_00005wcx

Streptococcus pyogenes phosphoglycerol transferase GacH in complex with sn-glycerol-1-phosphate, crystal form 1

• PDB DOI: https://doi.org/10.2210/pdb5WCX/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-02 Released: 2018-07-11 
• Deposition Author(s): Edgar, R.J., Korotkova, N., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Phosphoglycerol transferase GacH from Streptococcus pyogenes

Edgar, R.J., Korotkov, K.V., Korotkova, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 86.99 kDa 
• Atom Count: 6,421 
• Modeled Residue Count: 762 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerol transferase GacH	A, B	383	Streptococcus pyogenes serotype M1	Mutation(s): 0  Gene Names: SPy_0793
UniProt
Find proteins for Q9A0F9 (Streptococcus pyogenes serotype M1) Explore Q9A0F9  Go to UniProtKB:  Q9A0F9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1GP	D [auth A], G [auth B]	SN-GLYCEROL-1-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-VKHMYHEASA-N
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.97	α = 90
b = 77.53	β = 90
c = 174.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Edgar, R.J., Korotkova, N., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description