9JVA | pdb_00009jva

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

PDB DOI: https://doi.org/10.2210/pdb9JVA/pdb

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

Deposited: 2024-10-08 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: 2.08 Å
R-Value Free:
0.195 (Depositor), 0.189 (DCC)
R-Value Work:
0.166 (Depositor), 0.161 (DCC)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Cystathionine beta-lyase(PatB)/PLP complex of Lactobacillus lactobacillus delbrueckii at 1.53 ANG

Liu, Y., Yang, C.

To be published.

Macromolecule Content

Total Structure Weight: 88.61 kDa
Atom Count: 6,855
Modeled Residue Count: 774
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.195 (Depositor), 0.189 (DCC)
R-Value Work: 0.166 (Depositor), 0.161 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.661	α = 90
b = 94.218	β = 126.97
c = 84.762	γ = 90

Software Package:

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