6IQM

Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with NAD+ from Lactobacillus plantarum

• PDB DOI: https://doi.org/10.2210/pdb6IQM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-08 Released: 2018-11-21 
• Deposition Author(s): Yoneda, K., Kinoshita, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.190 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase from Lactobacillus plantarum: Insight into the Mercury Binding Mechanism

Yoneda, K., Ogata, M., Nishiyama, K., Fukuda, K., Yasuda, S., Igoshi, K., Kinoshita, H.

(2019) Milk Sci 68: 3-11

• DOI: https://doi.org/10.11465/milk.68.3

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: 148.99 kDa 
• Atom Count: 11,450 
• Modelled Residue Count: 1,336 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, type I	A, B, C, D	340	Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437	Mutation(s): 0  Gene Names: gap, HMPREF0531_11006 EC: 1.2.1.12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], I [auth B], K [auth C], M [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
TRS	H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	F [auth A], G [auth A], J [auth B], L [auth C], N [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.190 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.207	α = 90
b = 171.953	β = 90
c = 149.752	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Yoneda, K., Kinoshita, H.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description