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), 0.308 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9K71

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.308 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.