7YSL | pdb_00007ysl

Crystal structure of D-Cysteine desulfhydrase with a trapped PLP-pyruvate geminal diamine

• PDB DOI: https://doi.org/10.2210/pdb7YSL/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: 2.02 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (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: 80.84 kDa 
• Atom Count: 5,546 
• Modeled Residue Count: 676 
• 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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	C [auth A], F [auth A], G [auth A], H [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
EXA	A, B	PEPTIDE LINKING	C17 H27 N4 O9 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.38	α = 90
b = 85.478	β = 90
c = 123.091	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
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 2.0: 2023-02-08
  Changes: Atomic model, Derived calculations
• Version 3.0: 2023-11-29
  Changes: Data collection, Polymer sequence, Refinement description, Structure summary