5V8Y | pdb_00005v8y

Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

• PDB DOI: https://doi.org/10.2210/pdb5V8Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus agalactiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-22 Released: 2018-02-28 
• Deposition Author(s): Schormann, N., Ulett, G.C., Chattopadhyay, D.
• Funding Organization(s): Australian Res Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Schormann, N., Ulett, G.C., Chattopadhyay, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.16 kDa 
• Atom Count: 5,472 
• Modeled Residue Count: 665 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B	355	Streptococcus agalactiae	Mutation(s): 1  Gene Names: gap, AX245_09885, DX05_09270, EN72_09590, RDF_1710, TH70_1537 EC: 1.2.1
UniProt
Find proteins for Q9ALW2 (Streptococcus agalactiae) Explore Q9ALW2  Go to UniProtKB:  Q9ALW2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.081	α = 90
b = 147.081	β = 90
c = 72.283	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Schormann, N., Ulett, G.C., Chattopadhyay, D.

---

Funding Organization	Location	Grant Number
Australian Res Council	Australia	FT110101048

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description