8WWZ | pdb_00008wwz

Crystal structure of Bacillus subtilis glyceraldehyde-3-phosphate dehydrogenase GapB

• PDB DOI: https://doi.org/10.2210/pdb8WWZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-27 Released: 2024-10-02 
• Deposition Author(s): Dahal, P., Pathak, D., Kwon, E., Kim, D.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Bacillus subtilis glyceraldehyde-3-phosphate dehydrogenase GapB

Dahal, P., Pathak, D., Kwon, E.

(2023) Korean Soc Struct Biology 11: 59-65

• DOI: https://doi.org/10.34184/kssb.2023.11.4.59

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: 37.67 kDa 
• Atom Count: 2,602 
• Modeled Residue Count: 325 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase 2	A	342	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: gapB EC: 1.2.1.59
UniProt
Find proteins for O34425 (Bacillus subtilis (strain 168)) Explore O34425  Go to UniProtKB:  O34425

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.6	α = 90
b = 102.6	β = 90
c = 111.081	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Dahal, P., Pathak, D., Kwon, E., Kim, D.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release