9K71 | pdb_00009k71

Three-dimensional structure of homo-dimer of cystathione beta lyase/PLP from Bacillus cereus(BcPatB)

PDB DOI: https://doi.org/10.2210/pdb9K71/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Bacillus cereus ATCC 14579
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-10-23 Released: 2024-11-20
Deposition Author(s): Liu, Y., Yang, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.310 (Depositor), 0.310 (DCC)
R-Value Work:
0.229 (Depositor), 0.229 (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

Homodimer of cystatohinine beta lyase PatB/PLP complex from Bacillus cereus

Liu, Y., Yang, C.

To be published.

Macromolecule Content

Total Structure Weight: 88.78 kDa
Atom Count: 6,343
Modeled Residue Count: 765
Deposited Residue Count: 766
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cysteine-S-conjugate beta-lyase	A, B	383	Bacillus cereus ATCC 14579	Mutation(s): 19 Gene Names: BC_4906 EC: 4.4.1.13
UniProt
Find proteins for A0A9X7GT53 (Bacillus cereus) Explore A0A9X7GT53 Go to UniProtKB: A0A9X7GT53
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9X7GT53
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.28 Å
R-Value Free: 0.310 (Depositor), 0.310 (DCC)
R-Value Work: 0.229 (Depositor), 0.229 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.421	α = 90
b = 84.652	β = 90
c = 163.376	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	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
Other government	China	2021CXGC010803

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.