8PO5

Lactobacillus plantarum LpdD

• PDB DOI: https://doi.org/10.2210/pdb8PO5/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Lactobacillus
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S
• Mutation(s): No 


• Deposited: 2023-07-03 Released: 2024-01-17 
• Deposition Author(s): Gahloth, D., Leys, D.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Gallate decarboxylase subunit D, LpdD

Gahloth, D., Leys, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.86 kDa 
• Atom Count: 2,063 
• Modelled Residue Count: 249 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LpdD	A, B	142	Lactobacillus	Mutation(s): 0  Gene Names: lpdD, lp_0272
UniProt
Find proteins for F9UT68 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UT68  Go to UniProtKB:  F9UT68

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.5	α = 90
b = 92.98	β = 90
c = 126.82	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Gahloth, D., Leys, D.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release