5UTL | pdb_00005utl

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

• PDB DOI: https://doi.org/10.2210/pdb5UTL/pdb

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


• Deposited: 2017-02-15 Released: 2018-03-07 
• Deposition Author(s): Schormann, N., Ulett, G.C., Chattopadhyay, D.
• Funding Organization(s): Australian Res. Council (AU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Mutant Structures of Streptococcus agalactiae 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)

Macromolecule Content 

• Total Structure Weight: 155.55 kDa 
• Atom Count: 10,777 
• Modeled Residue Count: 1,346 
• Deposited Residue Count: 1,424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	356	Streptococcus agalactiae	Mutation(s): 1  Gene Names: gapA, gap, AMR84_09125, AX245_09885, BBP08_10800, DX05_09270, EN72_09590, ERS039640_00200, RDF_1710, TH70_1537 EC: 1.2.1
UniProt
Find proteins for Q9ALW2 (Streptococcus agalactiae) Explore Q9ALW2  Go to UniProtKB:  Q9ALW2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.826	α = 90
b = 108.412	β = 106.15
c = 90.44	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Schormann, N., Ulett, G.C., Chattopadhyay, D.

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Funding Organization	Location	Grant Number
Australian Res. Council (AU)	Australia	FT110101048

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description