9M0Q | pdb_00009m0q

The Structural Complex of Inactivated Lactobacillus delbrueckii Cystathionine beta-Lyase Mutant (LdPatB A34D) with Its Substrate L-(+)-Alliin

PDB DOI: https://doi.org/10.2210/pdb9M0Q/pdb

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

Deposited: 2025-02-25 Released: 2025-03-26
Deposition Author(s): Liu, Y., Yang, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.303 (Depositor), 0.303 (DCC)
R-Value Work:
0.251 (Depositor), 0.251 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Structural Complex of Inactivated Lactobacillus delbrueckii Cystathionine beta-Lyase Mutant (LdPatB A34D) with Its Substrate L-(+)-Alliin

Liu, Y., Yang, C.

To be published.

Macromolecule Content

Total Structure Weight: 88.84 kDa
Atom Count: 6,200
Modeled Residue Count: 763
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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): 3 Gene Names: LDL72_07215 EC: 4.4.1.13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OO0 Query on OO0 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ALLIIN C₆ H₁₁ N O₃ S XUHLIQGRKRUKPH-ULHQUTTKSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.303 (Depositor), 0.303 (DCC)
R-Value Work: 0.251 (Depositor), 0.251 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.831	α = 90
b = 91.682	β = 125.06
c = 80.871	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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 R01GM157729.