6J98 | pdb_00006j98

Crystal structure of P8 from Lactobacillus rhamnosus

• PDB DOI: https://doi.org/10.2210/pdb6J98/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Lacticaseibacillus rhamnosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-22 Released: 2020-03-04 
• Deposition Author(s): Cha, Y.J., Cho, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.196 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of P8 from Lactobacillus rhamnosus

Cha, Y.J., Cho, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 9.67 kDa 
• Atom Count: 699 
• Modeled Residue Count: 75 
• Deposited Residue Count: 77 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P8	A	77	Lacticaseibacillus rhamnosus	Mutation(s): 0  Gene Names: B4Q13_10920, BGK71_11245, CCE29_09795, DBP98_10520, PY66_06245, PY91_09235
UniProt
Find proteins for A0A0E3CPJ0 (Lacticaseibacillus rhamnosus) Explore A0A0E3CPJ0  Go to UniProtKB:  A0A0E3CPJ0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.196 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.86	α = 90
b = 40.86	β = 90
c = 107.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Cha, Y.J., Cho, H.S.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary