4RKQ | pdb_00004rkq

Crystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007

• PDB DOI: https://doi.org/10.2210/pdb4RKQ/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Arthrobacter sp. FB24
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-13 Released: 2014-11-12 
• 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., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal Structure of LacI Transcriptional Regulator PurR from Arthrobacter Sp, Target Nysgxrc 11027R

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., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

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: 124.26 kDa 
• Atom Count: 8,685 
• Modeled Residue Count: 1,091 
• Deposited Residue Count: 1,176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A, B, C, D	294	Arthrobacter sp. FB24	Mutation(s): 0  Gene Names: Arth_3918
UniProt
Find proteins for A0ACD6B8D2 (Arthrobacter sp. (strain FB24)) Explore A0ACD6B8D2  Go to UniProtKB:  A0ACD6B8D2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], I [auth B], J [auth C], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.244	α = 90
b = 125.126	β = 96.68
c = 116.422	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
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., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2018-01-31
  Changes: Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references