9JWC | pdb_00009jwc

Three-dimensional structure of homo-dimer of cystathione beta lyase/PLP/+L-alliin complex from lactobacillus delbrueckii(LdPatB)

• PDB DOI: https://doi.org/10.2210/pdb9JWC/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Lactobacillus delbrueckii subsp. lactis DSM 20072
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-10-10 Released: 2024-11-20 
• Deposition Author(s): Liu, Y., Yang, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.218 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.179 (DCC) 

Starting Model: in silico

Literature

Cystathionine beta-lyase(PatB)of Lactobacillus lactobacillus delbrueckii at 1.78 ?

Liu, Y., Yang, C.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.79 kDa 
• Atom Count: 6,701 
• Modeled Residue Count: 776 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cysteine-S-conjugate beta-lyase	A, B	390	Lactobacillus delbrueckii subsp. lactis DSM 20072	Mutation(s): 2  Gene Names: LDL72_07215 EC: 4.4.1.13
UniProt
Find proteins for Q1GA02 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)) Explore Q1GA02  Go to UniProtKB:  Q1GA02

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
OO0	C [auth A]	ALLIIN C6 H11 N O3 S XUHLIQGRKRUKPH-ULHQUTTKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.218 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.179 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.102	α = 90
b = 92	β = 126.05
c = 81.586	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Liu, Y., Yang, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	Project no. 42077214

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release