3IB5 | pdb_00003ib5

Crystal structure of Sex pheromone precursor (YP_536235.1) from LACTOBACILLUS SALIVARIUS SUBSP. SALIVARIUS UCC118 at 1.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IB5/pdb

• Classification: HORMONE
• Organism(s): Ligilactobacillus salivarius UCC118
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-15 Released: 2009-08-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal structure of Sex pheromone precursor (YP_536235.1) from LACTOBACILLUS SALIVARIUS SUBSP. SALIVARIUS UCC118 at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Macromolecule Content 

• Total Structure Weight: 39.07 kDa 
• Atom Count: 3,607 
• Modeled Residue Count: 342 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sex pheromone precursor	A	348	Ligilactobacillus salivarius UCC118	Mutation(s): 0  Gene Names: LSL_1347, YP_536235.1
UniProt
Find proteins for Q1WSH7 (Ligilactobacillus salivarius (strain UCC118)) Explore Q1WSH7  Go to UniProtKB:  Q1WSH7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	F [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IB5

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.175	α = 90
b = 82.175	β = 90
c = 108.295	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary