8JZJ

E.coli Glyceraldehyde-3-phosphate dehydrogenase structure under cryoprotect condition of ammonium sulfate

• PDB DOI: https://doi.org/10.2210/pdb8JZJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-05 Released: 2024-02-14 
• Deposition Author(s): Jang, K., Hlaing, S.H.S., Kim, H.G., Kim, N., Choe, H.W., Kim, Y.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Strategy to Select an Appropriate Cryoprotectant for an X-ray Study of Escherichia coli GAPDH Crystals

Hlaing, S.H.S., Jang, K., Kim, H.G., Kim, N., Lee, K.J., Choe, H.W., Park, J.H., Kim, Y.J.

(2023) Cryst Growth Des 23: 7126-7133

• DOI: https://doi.org/10.1021/acs.cgd.3c00483

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.54 kDa 
• Atom Count: 2,755 
• Modelled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A	330	Escherichia coli	Mutation(s): 0  Gene Names: gapA EC: 1.2.1.12
UniProt
Find proteins for P0A9B2 (Escherichia coli (strain K12)) Explore P0A9B2  Go to UniProtKB:  P0A9B2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.971	α = 90
b = 121.971	β = 90
c = 155.134	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Jang, K., Hlaing, S.H.S., Kim, H.G., Kim, N., Choe, H.W., Kim, Y.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A3060013

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Database references