4WXE | pdb_00004wxe

CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS

• PDB DOI: https://doi.org/10.2210/pdb4WXE/pdb

• Classification: TRANSCRIPTION
• Organism(s): Lacticaseibacillus paracasei ATCC 334
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-13 Released: 2014-11-26 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.168 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.58 kDa 
• Atom Count: 2,594 
• Modeled Residue Count: 278 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A	303	Lacticaseibacillus paracasei ATCC 334	Mutation(s): 0  Gene Names: LSEI_2103
UniProt
Find proteins for Q036L9 (Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 / NRRL B-441)) Explore Q036L9  Go to UniProtKB:  Q036L9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [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: 1.50 Å
• R-Value Free:  0.168 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.047	α = 90
b = 108.047	β = 90
c = 121.477	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Experimental preparation
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary