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), 0.188 (DCC)
R-Value Work:
0.166 (Depositor), 0.162 (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

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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(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

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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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), 0.188 (DCC)
R-Value Work: 0.166 (Depositor), 0.162 (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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Ligand Structure Quality Assessment

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.