8Y54 | pdb_00008y54

Three-dimensional structure of homo-dimer of cystathione beta lyase from lactobacillus delbrueckii(LdPatB)

PDB DOI: https://doi.org/10.2210/pdb8Y54/pdb

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

Deposited: 2024-01-31 Released: 2024-11-20
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: 1.78 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.207 (Depositor), 0.206 (DCC)

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

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

Literature

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

Liu, Y., Yang, C.

To be published.

Macromolecule Content

Total Structure Weight: 88.12 kDa
Atom Count: 6,490
Modeled Residue Count: 773
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): 2 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.207 (Depositor), 0.206 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.47	α = 90
b = 91.06	β = 125.27
c = 80.87	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

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: 2024-11-20
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.