7YSK | pdb_00007ysk

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 (Depositor), 0.268 (DCC)
R-Value Work:
0.223 (Depositor), 0.222 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 675
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

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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 (PDB Primary Data), 4.4.1.25 (UniProt)
UniProt
Find proteins for Q6D6Z8 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D6Z8 Go to UniProtKB: Q6D6Z8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.268 (DCC)
R-Value Work: 0.223 (Depositor), 0.222 (DCC)
R-Value Observed: 0.225 (Depositor)

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

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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

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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.