7WWW | pdb_00007www

Crystal Structure of Moonlighting GAPDH protein of Lactobacillus gasseri

• PDB DOI: https://doi.org/10.2210/pdb7WWW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactobacillus gasseri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-14 Released: 2023-02-22 
• Deposition Author(s): Jeng, W.Y., Chen, P.C., Wang, J.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.130 (DCC) 

Starting Model: experimental

Literature

Moonlighting GAPDH protein of Lactobacillus gasseri attenuates allergic asthma via immunometabolism change in macrophages

Chen, P.C., Hsieh, M.H., Kuo, W.S., Wu, L.S.H., Kao, H.F., Liu, L.F., Liu, Z.G., Jeng, W.Y., Wang, J.Y.

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: 38.14 kDa 
• Atom Count: 2,829 
• Modeled Residue Count: 336 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A	346	Lactobacillus gasseri	Mutation(s): 0  Gene Names: gap, BXT97_01160, C3745_09540, F8244_01270, GTH50_07620
UniProt
Find proteins for A0A1V3Y2M1 (Lactobacillus gasseri) Explore A0A1V3Y2M1  Go to UniProtKB:  A0A1V3Y2M1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.130 (DCC) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.922	α = 90
b = 114.922	β = 90
c = 118.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Jeng, W.Y., Chen, P.C., Wang, J.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	NSC 102-2311-B-006-006-MY3
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	107-2314-B-006 -046 -MY3

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description