4XCH | pdb_00004xch

S-ribosylhomocysteinase from Streptococcus suis

• PDB DOI: https://doi.org/10.2210/pdb4XCH/pdb

• Classification: LYASE
• Organism(s): Streptococcus suis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-18 Released: 2015-06-24 
• Deposition Author(s): Wang, Y., Mao, X., Lu, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal Structure of LuxS from Streptococcus suis

Wang, Y., Mao, X., Lu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 86.53 kDa 
• Atom Count: 4,825 
• Modeled Residue Count: 596 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-ribosylhomocysteine lyase	A, B, C, D	194	Streptococcus suis	Mutation(s): 0  Gene Names: luxS EC: 4.4.1.21
UniProt
Find proteins for B2CMA5 (Streptococcus suis) Explore B2CMA5  Go to UniProtKB:  B2CMA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.89	α = 90
b = 86.25	β = 90
c = 103.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data processing
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): Wang, Y., Mao, X., Lu, C.

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations