4RK5 | pdb_00004rk5

Crystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound sucrose

• PDB DOI: https://doi.org/10.2210/pdb4RK5/pdb

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


• Deposited: 2014-10-11 Released: 2014-11-05 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.141 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.109 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.110 (Depositor) 

Literature

Crystal Structure of LacI Transcriptional Regulator Lsei_2103 from Lactobacillus casei, Target EFI-512911

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C.

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: 31.34 kDa 
• Atom Count: 2,486 
• Modeled Residue Count: 275 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A	283	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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.141 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.109 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.110 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.754	α = 90
b = 108.754	β = 90
c = 125.763	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary