4RK0

Crystal structure of LacI family transcriptional regulator from Enterococcus faecalis V583, Target EFI-512923, with bound ribose

• PDB DOI: https://doi.org/10.2210/pdb4RK0/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-11 Released: 2014-10-29 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Crystal Structure of LacI Transcriptional Regulator Ef_2962 from Enterococcus faecalis V583, Target EFI-512923

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 123.86 kDa 
• Atom Count: 9,006 
• Modelled Residue Count: 1,072 
• Deposited Residue Count: 1,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LacI family sugar-binding transcriptional regulator	A, B, C, D	274	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_2962, I574_00070, OO5_00598
UniProt
Find proteins for Q82ZT5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q82ZT5  Go to UniProtKB:  Q82ZT5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIB	E [auth A], F [auth B], G [auth C], H [auth D]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.919	α = 87.72
b = 77.234	β = 82.57
c = 91.805	γ = 84.33

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
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: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary