8P4W

Lactobacillus plantarum LpdD mutant - H35A

PDB DOI: https://doi.org/10.2210/pdb8P4W/pdb

Classification: FLAVOPROTEIN
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No

Deposited: 2023-05-23 Released: 2024-06-12
Deposition Author(s): Gahloth, D., Leys, D.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.220
R-Value Work: 0.194
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Gallate decarboxylase subunit D, LpdD

Gahloth, D., Leys, D.

To be published.

Macromolecule Content

Total Structure Weight: 15.14 kDa
Atom Count: 1,068
Modelled Residue Count: 120
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LpdD	A	136	Lactiplantibacillus plantarum	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9UT68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.220
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 58.97	β = 90
c = 83.38	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-06-12
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.