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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

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

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.270 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Zhang, X., Wang, L., Xu, X., Xing, X., Zhou, J.

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

Revision History  

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