7YSK

Crystal structure of D-Cysteine desulfhydrase from Pectobacterium atrosepticum

PDB DOI: https://doi.org/10.2210/pdb7YSK/pdb

Classification: LYASE
Organism(s): Pectobacterium atrosepticum SCRI1043
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-08-12 Released: 2022-12-14
Deposition Author(s): Zhang, X., Wang, L., Xu, X., Xing, X., Zhou, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.268
R-Value Work: 0.223
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Characterization and structural basis of D-cysteine desulfhydrase from Pectobacterium atrosepticum

Xu, X., Yang, L., Zhang, X., Xing, X., Zhou, J.

(2022) Tetrahedron : 133174

DOI: https://doi.org/10.1016/j.tet.2022.133174

Macromolecule Content

Total Structure Weight: 79.93 kDa
Atom Count: 5,660
Modelled Residue Count: 675
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Cysteine desulfhydrase	A, B	371	Pectobacterium atrosepticum SCRI1043	Mutation(s): 0 Gene Names: ECA1531 EC: 4.4.1.15
UniProt
Find proteins for Q6D6Z8 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D6Z8 Go to UniProtKB: Q6D6Z8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6D6Z8
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: 1.80 Å
R-Value Free: 0.268
R-Value Work: 0.223
R-Value Observed: 0.225
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.474	α = 90
b = 86.54	β = 90.45
c = 68.482	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA09005000

Revision History (Full details and data files)

Version 1.0: 2022-12-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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 R01GM133198.