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)

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.0 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: 80.84 kDa
Atom Count: 5,546
Modeled Residue Count: 676
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

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| 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 (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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A]	D [auth A], E [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	C [auth A] F [auth A] G [auth A] H [auth A] J [auth A] 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		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
EXA Query on 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)
R-Value Work: 0.172 (Depositor)
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

View Full Validation Report

View more in-depth experimental data

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 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