5V2W | pdb_00005v2w

Crystal structure of a LuxS from salmonella typhi

• PDB DOI: https://doi.org/10.2210/pdb5V2W/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-06 Released: 2017-08-23 
• Deposition Author(s): Perumal, P., Raina, R., Manoj Kumar, P., Arockisamy, A., SundaraBaalaji, N.
• Funding Organization(s): ICMR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a LuxS from salmonella typhi

Perumal, P., Raina, R., Arockisamy, A., SundaraBaalaji, N.

To be published.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.01 kDa 
• Atom Count: 2,670 
• Modeled Residue Count: 339 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-ribosylhomocysteine lyase	A, B	179	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 1  Gene Names: luxS, STY2943, t2714 EC: 4.4.1.21
UniProt
Find proteins for Q8Z4D7 (Salmonella typhi) Explore Q8Z4D7  Go to UniProtKB:  Q8Z4D7

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.33	α = 90
b = 65.453	β = 106.55
c = 54.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
PHENIX	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-23 
Deposition Author(s): Perumal, P., Raina, R., Manoj Kumar, P., Arockisamy, A., SundaraBaalaji, N.

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Funding Organization	Location	Grant Number
ICMR	India	2011-15260

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary