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), 0.231 (DCC)
R-Value Work:
0.207 (Depositor), 0.205 (DCC)

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

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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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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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.232 (Depositor), 0.231 (DCC)
R-Value Work: 0.207 (Depositor), 0.205 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.